For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o. delta-G'o = -RT lnK' and delta-G'o = delta-H'o - T delta-S'o delta-G'o has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'o T I pH pMg). This property may have multiple values, representing different measurements for delta-G'o obtained under the different experimental conditions listed in the 5-tuple. (This definition from EcoCyc)
A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types.
A cellular location, e.g. 'cytoplasm'. This should reference a term in the Gene Ontology Cellular Component ontology. The location referred to by this property should be as specific as is known. If an interaction is known to occur in multiple locations, separate interactions (and physicalEntityParticipants) must be created for each different location. Note: If a location is unknown then the GO term for 'cellular component unknown' (GO:0008372) should be used in the LOCATION property. If the location of a participant in a complex is unspecified, it may be assumed to be the same location as that of the complex. In case of conflicting information, the location of the most outer layer of any nesting should be considered correct. Note: Cellular location describes a specific location of a physical entity as it would be used in e.g. a transport reaction. It does not describe all of the possible locations that the physical entity could be in the cell.
Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. COFACTOR is a sub-property of PARTICIPANTS.
Defines the physicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the COMPONENTS of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the COMPONENTS property is empty), which may be used as COMPONENTS of other complexes (via a physicalEntityParticipant instance) because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order.
Confidence in the containing instance. Usually a statistical measure.
The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. CONTROLLED is a sub-property of PARTICIPANTS.
The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. CONTROLLER is a sub-property of PARTICIPANTS.
A free text description of the source of this data, e.g. a database or person name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation.
Scientific evidence supporting the existence of the entity as described.
A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
The experimental forms associated with an evidence instance.
Descriptor of this experimental form from a controlled vocabulary.
Location of the feature on the sequence of the interactor. One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence.
Description and classification of the feature.
External controlled vocabulary characterizing the interaction type, for example "phosphorylation".
This quantity is dimensionless and is usually a single number. The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K' = [ADP][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [MgHATP-] + [Mg2ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm3) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc)
The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the LEFT property may be either reactants or products. LEFT is a sub-property of PARTICIPANTS.
The next step(s) of the pathway. Contains zero or more pathwayStep instances. If there is no next step, this property is empty.
An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
The participant that has the experimental form being described.
This property lists the entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. This property has a number of sub-properties, such as LEFT and RIGHT in the biochemicalInteraction class. Any participant listed in a sub-property will automatically be assumed to also be in PARTICIPANTS by a number of software systems, including Protégé, so this property should not contain any instances if there are instances contained in a sub-property.
The set of interactions and/or pathwaySteps in this pathway/network. Each instance of the pathwayStep class defines: 1) a set of interactions that together define a particular step in the pathway, for example a catalysis instance and the conversion that it catalyzes; 2) an order relationship to one or more other pathway steps (via the NEXT-STEP property). Note: This ordering is not necessarily temporal - the order described may simply represent connectivity between adjacent steps. Temporal ordering information should only be inferred from the direction of each interaction.
The physical entity annotated with stoichiometry and cellular location attributes from the physicalEntityParticipant instance.
The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the RIGHT property may be either reactants or products. RIGHT is a sub-property of PARTICIPANTS.
Sequence features relevant for the interaction, for example binding domains or modification sites. Warning: this property may be moved into a state class in Level 3.
The begin position of a sequence interval.
The end position of a sequence interval.
The interactions that take place at this step of the pathway.
Defines the chemical structure and other information about this molecule, using an instance of class chemicalStructure.
An xref to an organism taxonomy database, preferably NCBI taxon. This should be an instance of unificationXref, unless the organism is not in an existing database.
An external controlled vocabulary of tissue types.
Values of this property define external cross-references from this entity to entities in external databases.
The authors of this publication, one per property value.
Describes the availability of this data (e.g. a copyright statement).
The chemical formula of the small molecule. Note: chemical formula can also be stored in the STRUCTURE property (in CML). In case of disagreement between the value of this property and that in the CML file, the CML value takes precedence.
Comment on the data in the container class. This property should be used instead of the OWL documentation elements (rdfs:comment) for instances because information in COMMENT is data to be exchanged, whereas the rdfs:comment field is used for metadata about the structure of the BioPAX ontology.
Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities. The following terms are possible values: ACTIVATION: General activation. Compounds that activate the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. The following term can not be used in the catalysis class: INHIBITION: General inhibition. Compounds that inhibit the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. The following terms can only be used in the modulation class (these definitions from EcoCyc): INHIBITION-ALLOSTERIC Allosteric inhibitors decrease the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that decreases the affinity of the enzyme to its substrates without affecting its VMAX. Allosteric inhibitors can be competitive or noncompetitive inhibitors, therefore, those inhibition categories can be used in conjunction with this category. INHIBITION-COMPETITIVE Competitive inhibitors are compounds that competitively inhibit the specified enzyme activity by binding reversibly to the enzyme and preventing the substrate from binding. Binding of the inhibitor and substrate are mutually exclusive because it is assumed that the inhibitor and substrate can both bind only to the free enzyme. A competitive inhibitor can either bind to the active site of the enzyme, directly excluding the substrate from binding there, or it can bind to another site on the enzyme, altering the conformation of the enzyme such that the substrate can not bind to the active site. INHIBITION-IRREVERSIBLE Irreversible inhibitors are compounds that irreversibly inhibit the specified enzyme activity by binding to the enzyme and dissociating so slowly that it is considered irreversible. For example, alkylating agents, such as iodoacetamide, irreversibly inhibit the catalytic activity of some enzymes by modifying cysteine side chains. INHIBITION-NONCOMPETITIVE Noncompetitive inhibitors are compounds that noncompetitively inhibit the specified enzyme by binding reversibly to both the free enzyme and to the enzyme-substrate complex. The inhibitor and substrate may be bound to the enzyme simultaneously and do not exclude each other. However, only the enzyme-substrate complex (not the enzyme-substrate-inhibitor complex) is catalytically active. INHIBITION-OTHER Compounds that inhibit the specified enzyme activity by a mechanism that has been characterized, but that cannot be clearly classified as irreversible, competitive, noncompetitive, uncompetitive, or allosteric. INHIBITION-UNCOMPETITIVE Uncompetitive inhibitors are compounds that uncompetitively inhibit the specified enzyme activity by binding reversibly to the enzyme-substrate complex but not to the enzyme alone. ACTIVATION-NONALLOSTERIC Nonallosteric activators increase the specified enzyme activity by means other than allosteric. ACTIVATION-ALLOSTERIC Allosteric activators increase the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that increases the affinity of the enzyme to its substrates without affecting its VMAX.
The name of the external database to which this xref refers.
The version of the external database in which this xref was last known to be valid. Resources may have recommendations for referencing dataset versions. For instance, the Gene Ontology recommends listing the date the GO terms were downloaded.
For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o. delta-G'o = -RT lnK' and delta-G'o = delta-H'o - T delta-S'o delta-G'o has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'o T I pH pMg). (This definition from EcoCyc)
For biochemical reactions, this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'o. delta-G'o = delta-H'o - T delta-S'o Units: kJ/mole (This definition from EcoCyc)
For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'o. delta-G'o = delta-H'o - T delta-S'o (This definition from EcoCyc)
Specifies the reaction direction of the interaction catalyzed by this instance of the catalysis class. Possible values of this slot are: REVERSIBLE: Interaction occurs in both directions in physiological settings. PHYSIOL-LEFT-TO-RIGHT PHYSIOL-RIGHT-TO-LEFT The interaction occurs in the specified direction in physiological settings, because of several possible factors including the energetics of the reaction, local concentrations of reactants and products, and the regulation of the enzyme or its expression. IRREVERSIBLE-LEFT-TO-RIGHT IRREVERSIBLE-RIGHT-TO-LEFT For all practical purposes, the interactions occurs only in the specified direction in physiological settings, because of chemical properties of the reaction. (This definition from EcoCyc)
The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology. Note that not all biochemical reactions currently have EC numbers assigned to them.
The primary identifier in the external database of the object to which this xref refers.
The version number of the identifier (ID). E.g. The RefSeq accession number NM_005228.3 should be split into NM_005228 as the ID and 3 as the ID-VERSION.
The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi). For example, the ionic strength of a 0.1 M solution of CaCl2 is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3 M (Definition from http://www.lsbu.ac.uk/biology/enztech/ph.html)
The apparent equilibrium constant K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K' = [ADP][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [MgHATP-] + [Mg2ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm3) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). (Definition from EcoCyc)
Defines the molecular weight of the molecule, in daltons.
The preferred full name for this entity.
A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution. (Definition from Merriam-Webster Dictionary)
A measure of the concentration of magnesium (Mg) in solution. (pMg = -log10[Mg2+])
The confidence status of the sequence position. This could be: EQUAL: The SEQUENCE-POSITION is known to be at the SEQUENCE-POSITION. GREATER-THAN: The site is greater than the SEQUENCE-POSITION. LESS-THAN: The site is less than the SEQUENCE-POSITION.
This property names the type of relationship between the BioPAX object linked from, and the external object linked to, such as 'gene of this protein', or 'protein with similar sequence'.
Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.
The integer listed gives the position. The first base or amino acid is position 1. In combination with the numeric value, the property 'POSITION-STATUS' allows to express fuzzy positions, e.g. 'less than 4'.
An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.
The source in which the reference was published, such as: a book title, or a journal title and volume and pages.
Specifies whether a conversion occurs spontaneously (i.e. uncatalyzed, under biological conditions) left-to-right, right-to-left, or not at all. If the spontaneity is not known, the SPONTANEOUS property should be left empty.
Each value of this property represents the stoichiometric coefficient for one of the physical entities in an interaction or complex. For a given interaction, the stoichiometry should always be used where possible instead of representing the number of participants with separate instances of each participant. If there are three ATP molecules, one ATP molecule should be represented as a participant and the stoichiometry should be set to 3.
This property holds a string of data defining chemical structure or other information, in either the CML or SMILES format, as specified in property Structure-Format. If, for example, the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.
This property specifies which format is used to define chemical structure data.
One or more synonyms for the name of this entity. This should include the values of the NAME and SHORT-NAME property so that it is easy to find all known names in one place.
The external controlled vocabulary term.
The title of the publication.
The URL at which the publication can be found, if it is available through the Web.
The year in which this publication was published.
Definition: The biological source of an entity (e.g. protein, RNA or DNA). Some entities are considered source-neutral (e.g. small molecules), and the biological source of others can be deduced from their constituentss (e.g. complex, pathway). Examples: HeLa cells, human, and mouse liver tissue.
Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). The substrates of biochemical reactions are defined in terms of sums of species. This is convention in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions. Examples: ATP + H2O = ADP + Pi Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen.
Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. Instances of this class describe a pairing between a catalyzing entity and a catalyzed conversion. Comment: A separate catalysis instance should be created for each different conversion that a physicalEntity may catalyze and for each different physicalEntity that may catalyze a conversion. For example, a bifunctional enzyme that catalyzes two different biochemical reactions would be linked to each of those biochemical reactions by two separate instances of the catalysis class. Also, catalysis reactions from multiple different organisms could be linked to the same generic biochemical reaction (a biochemical reaction is generic if it only includes small molecules). Generally, the enzyme catalyzing a conversion is known and the use of this class is obvious. In the cases where a catalyzed reaction is known to occur but the enzyme is not known, a catalysis instance should be created without a controller specified (i.e. the CONTROLLER property should remain empty). Synonyms: facilitation, acceleration. Examples: The catalysis of a biochemical reaction by an enzyme, the enabling of a transport interaction by a membrane pore complex, and the facilitation of a complex assembly by a scaffold protein. Hexokinase -> (The "Glucose + ATP -> Glucose-6-phosphate +ADP" reaction). A plasma membrane Na+/K+ ATPase is an active transporter (antiport pump) using the energy of ATP to pump Na+ out of the cell and K+ in. Na+ from cytoplasm to extracellular space would be described in a transport instance. K+ from extracellular space to cytoplasm would be described in a transport instance. The ATPase pump would be stored in a catalysis instance controlling each of the above transport instances. A biochemical reaction that does not occur by itself under physiological conditions, but has been observed to occur in the presence of cell extract, likely via one or more unknown enzymes present in the extract, would be stored in the CONTROLLED property, with the CONTROLLER property empty.
Definition: Describes a small molecule structure. Structure information is stored in the property STRUCTURE-DATA, in one of three formats: the CML format (see URL www.xml-cml.org), the SMILES format (see URL www.daylight.com/dayhtml/smiles/) or the InChI format (http://www.iupac.org/inchi/). The STRUCTURE-FORMAT property specifies which format is used. Comment: By virtue of the expressivity of CML, an instance of this class can also provide additional information about a small molecule, such as its chemical formula, names, and synonyms, if CML is used as the structure format. Examples: The following SMILES string, which describes the structure of glucose-6-phosphate: 'C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)'.
Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction. Comment: In general, complexes should not be defined recursively so that smaller complexes exist within larger complexes, i.e. a complex should not be a COMPONENT of another complex (see comments on the COMPONENT property). The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding and the topology of the components cannot be described currently, but may be included in future versions of the ontology, depending on community need. Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules.
Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g. protein, RNA, DNA), aggregate via non-covalent interactions. One of the participants of a complexAssembly must be an instance of the class complex (via a physicalEntityParticipant instance). Comment: This class is also used to represent complex disassembly. The assembly or disassembly of a complex is often a spontaneous process, in which case the direction of the complexAssembly (toward either assembly or disassembly) should be specified via the SPONTANEOUS property. Synonyms: aggregation, complex formation Examples: Assembly of the TFB2 and TFB3 proteins into the TFIIH complex, and assembly of the ribosome through aggregation of its subunits. Note: The following are not examples of complex assembly: Covalent phosphorylation of a protein (this is a biochemicalReaction); the TFIIH complex itself (this is an instance of the complex class, not the complexAssembly class).
Definition: Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure. The xref must contain at least on publication that describes the method used to determine the confidence. There is currently no standard way of describing confidence values, so any string is valid for the confidence value. In the future, a controlled vocabulary of accepted confidence values could become available, in which case it will likely be adopted for use here to describe the value. Examples: The statistical significance of a result, e.g. "p<0.05".
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition. Comment: In general, the targets of control processes (i.e. occupants of the CONTROLLED property) should be interactions. Conceptually, physical entities are involved in interactions (or events) and the events should be controlled or modified, not the physical entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an 'activation' arrow from the kinase to the substrate in signaling diagrams. This is an abstraction that can be ambiguous out of context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a reaction in which the substrate is phosphorylated, instead of as a control interaction in which the kinase activates the substrate. Since this class is a superclass for specific types of control, instances of the control class should only be created when none of its subclasses are applicable. Synonyms: regulation, mediation Examples: A small molecule that inhibits a pathway by an unknown mechanism controls the pathway.
Definition: An interaction in which one or more entities is physically transformed into one or more other entities. Comment: This class is designed to represent a simple, single-step transformation. Multi-step transformations, such as the conversion of glucose to pyruvate in the glycolysis pathway, should be represented as pathways, if known. Since it is a highly abstract class in the ontology, instances of the conversion class should never be created. Examples: A biochemical reaction converts substrates to products, the process of complex assembly converts single molecules to a complex, transport converts entities in one compartment to the same entities in another compartment.
Definition: The direct source of this data. This does not store the trail of sources from the generation of the data to this point, only the last known source, such as a database. The XREF property may contain a publicationXref referencing a publication describing the data source (e.g. a database publication). A unificationXref may be used e.g. when pointing to an entry in a database of databases describing this database. Examples: A database or person name.
Definition: For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o. delta-G'o = -RT lnK' and delta-G'o = delta-H'o - T delta-S'o delta-G'o has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'o T I pH pMg). This property may have multiple values, representing different measurements for delta-G'o obtained under the different experimental conditions listed in the 5-tuple. (This definition from EcoCyc)
Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. Comment: This is not a 'gene', since gene is a genetic concept, not a physical entity. The concept of a gene may be added later in BioPAX. Examples: a chromosome, a plasmid. A specific example is chromosome 7 of Homo sapiens.
Definition: A discrete biological unit used when describing pathways. Comment: This is the root class for all biological concepts in the ontology, which include pathways, interactions and physical entities. As the most abstract class in the ontology, instances of the entity class should never be created. Instead, more specific classes should be used. Synonyms: thing, object, bioentity.
Definition: The support for a particular assertion, such as the existence of an interaction or pathway. At least one of CONFIDENCE, EVIDENCE-CODE, or EXPERIMENTAL-FORM must be instantiated when creating an evidence instance. XREF may reference a publication describing the experimental evidence using a publicationXref or may store a description of the experiment in an experimental description database using a unificationXref (if the referenced experiment is the same) or relationshipXref (if it is not identical, but similar in some way e.g. similar in protocol). Evidence is meant to provide more information than just an xref to the source paper. Examples: A description of a molecular binding assay that was used to detect a protein-protein interaction.
Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design. Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms
Definition: A pointer to an external object, such as an entry in a database or a term in a controlled vocabulary. Comment: This class is for organizational purposes only; direct instances of this class should not be created.
Definition: A single biological relationship between two or more entities. An interaction cannot be defined without the entities it relates. Comment: Since it is a highly abstract class in the ontology, instances of the interaction class should never be created. Instead, more specific classes should be used. Currently this class only has subclasses that define physical interactions; later levels of BioPAX may define other types of interactions, such as genetic (e.g. synthetic lethal). Naming rationale: A number of names were considered for this concept, including "process", "synthesis" and "relationship"; Interaction was chosen as it is understood by biologists in a biological context and is compatible with PSI-MI. Examples: protein-protein interaction, biochemical reaction, enzyme catalysis
Definition: The apparent equilibrium constant, K', and associated values. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K' = [ADP][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [MgHATP-] + [Mg2ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm3) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc) See http://www.chem.qmul.ac.uk/iubmb/thermod/ for a thermodynamics tutorial.
Definition: A control interaction in which a physical entity modulates a catalysis interaction. Biologically, most modulation interactions describe an interaction in which a small molecule alters the ability of an enzyme to catalyze a specific reaction. Instances of this class describe a pairing between a modulating entity and a catalysis interaction. Comment: A separate modulation instance should be created for each different catalysis instance that a physical entity may modulate and for each different physical entity that may modulate a catalysis instance. A typical modulation instance has a small molecule as the controller entity and a catalysis instance as the controlled entity. Examples: Allosteric activation and competitive inhibition of an enzyme's ability to catalyze a specific reaction.
Definition: Used to import terms from external controlled vocabularies (CVs) into the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO) or other open biological CVs listed on the OBO website (http://obo.sourceforge.net/). Comment: The ID property in unification xrefs to GO and other OBO ontologies should include the ontology name in the ID property (e.g. ID="GO:0005634" instead of ID="0005634").
Definition: A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons. Comment: It is possible to define a pathway without specifying the interactions within the pathway. In this case, the pathway instance could consist simply of a name and could be treated as a 'black box'. Synonyms: network Examples: glycolysis, valine biosynthesis
Definition: A step in a pathway. Comment: Multiple interactions may occur in a pathway step, each should be listed in the STEP-INTERACTIONS property. Order relationships between pathway steps may be established with the NEXT-STEP slot. This order may not be temporally meaningful for specific steps, such as for a pathway loop or a reversible reaction, but represents a directed graph of step relationships that can be useful for describing the overall flow of a pathway, as may be useful in a pathway diagram. Example: A metabolic pathway may contain a pathway step composed of one biochemical reaction (BR1) and one catalysis (CAT1) instance, where CAT1 describes the catalysis of BR1.
Definition: An entity with a physical structure. A pool of entities, not a specific molecular instance of an entity in a cell. Comment: This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. As a highly abstract class in the ontology, instances of the physicalEntity class should never be created. Instead, more specific classes should be used. Synonyms: part, interactor, object Naming rationale: It's difficult to find a name that encompasses all of the subclasses of this class without being too general. E.g. PSI-MI uses 'interactor', BIND uses 'object', BioCyc uses 'chemicals'. physicalEntity seems to be a good name for this specialization of entity. Examples: protein, small molecule, RNA
Definition: Any additional special characteristics of a physical entity in the context of an interaction or complex. These currently include stoichiometric coefficient and cellular location, but this list may be expanded in later levels. Comment: PhysicalEntityParticipants should not be used in multiple interaction or complex instances. Instead, each interaction and complex should reference its own unique set of physicalEntityParticipants. The reason for this is that a user may add new information about a physicalEntityParticipant for one interaction or complex, such as the presence of a previously unknown post-translational modification, and unwittingly invalidate the physicalEntityParticipant for the other interactions or complexes that make use of it. Example: In the interaction describing the transport of L-arginine into the cytoplasm in E. coli, the LEFT property in the interaction would be filled with an instance of physicalEntityParticipant that specified the location of L-arginine as periplasm and the stoichiometric coefficient as one.
Definition: An interaction in which at least one participant is a physical entity, e.g. a binding event. Comment: This class should be used by default for representing molecular interactions, such as those defined by PSI-MI level 2. The participants in a molecular interaction should be listed in the PARTICIPANTS slot. Note that this is one of the few cases in which the PARTICPANT slot should be directly populated with instances (see comments on the PARTICPANTS property in the interaction class description). If sufficient information on the nature of a molecular interaction is available, a more specific BioPAX interaction class should be used. Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens.
Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain. Examples: The epidermal growth factor receptor (EGFR) protein.
Definition: An xref that defines a reference to a publication such as a book, journal article, web page, or software manual. The reference may or may not be in a database, although references to PubMed are preferred when possible. The publication should make a direct reference to the instance it is attached to. Comment: Publication xrefs should make use of PubMed IDs wherever possible. The DB property of an xref to an entry in PubMed should use the string "PubMed" and not "MEDLINE". Examples: PubMed:10234245
Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity. Comment: There is currently no controlled vocabulary of relationship types for BioPAX, although one will be created in the future if a need develops. Examples: A link between a gene G in a BioPAX data collection, and the protein product P of that gene in an external database. This is not a unification xref because G and P are different biological entities (one is a gene and one is a protein). Another example is a relationship xref for a protein that refers to the Gene Ontology biological process, e.g. 'immune response,' that the protein is involved in.
Definition: A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid. Examples: messengerRNA, microRNA, ribosomalRNA. A specific example is the let-7 microRNA.
Definition: A feature on a sequence relevant to an interaction, such as a binding site or post-translational modification. Examples: A phosphorylation on a protein.
Definition: Describes an interval on a sequence. All of the sequence from the begin site to the end site (inclusive) is described, not any subset.
Definition: A location on a nucleotide or amino acid sequence. Comment: For organizational purposes only; direct instances of this class should not be created.
Definition: A DNA, RNA or protein participant in an interaction. Comment: See physicalEntityParticipant for more documentation.
Definition: Describes a site on a sequence, i.e. the position of a single nucleotide or amino acid.
Definition: Any bioactive molecule that is not a peptide, DNA, or RNA. Generally these are non-polymeric, but complex carbohydrates are not explicitly modeled as classes in this version of the ontology, thus are forced into this class. Comment: Recently, a number of small molecule databases have become available to cross-reference from this class. Examples: glucose, penicillin, phosphatidylinositol
Definition: A conversion interaction in which an entity (or set of entities) changes location within or with respect to the cell. A transport interaction does not include the transporter entity, even if one is required in order for the transport to occur. Instead, transporters are linked to transport interactions via the catalysis class. Comment: Transport interactions do not involve chemical changes of the participant(s). These cases are handled by the transportWithBiochemicalReaction class. Synonyms: translocation. Examples: The movement of Na+ into the cell through an open voltage-gated channel.
Definition: A conversion interaction that is both a biochemicalReaction and a transport. In transportWithBiochemicalReaction interactions, one or more of the substrates change both their location and their physical structure. Active transport reactions that use ATP as an energy source fall under this category, even if the only covalent change is the hydrolysis of ATP to ADP. Comment: This class was added to support a large number of transport events in pathway databases that have a biochemical reaction during the transport process. It is not expected that other double inheritance subclasses will be added to the ontology at the same level as this class. Examples: In the PEP-dependent phosphotransferase system, transportation of sugar into an E. coli cell is accompanied by the sugar's phosphorylation as it crosses the plasma membrane.
Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity. For example, if one wished to link from a database record, C, describing a chemical compound in a BioPAX data collection to a record, C', describing the same chemical compound in an external database, one would use a unification xref since records C and C' describe the same biological identity. Generally, unification xrefs should be used whenever possible, although there are cases where they might not be useful, such as application to application data exchange. Comment: Unification xrefs in physical entities are essential for data integration, but are less important in interactions. This is because unification xrefs on the physical entities in an interaction can be used to compute the equivalence of two interactions of the same type. An xref in a protein pointing to a gene, e.g. in the LocusLink database17, would not be a unification xref since the two entities do not have the same biological identity (one is a protein, the other is a gene). Instead, this link should be a captured as a relationship xref. References to an external controlled vocabulary term within the OpenControlledVocabulary class should use a unification xref where possible (e.g. GO:0005737). Examples: An xref in a protein instance pointing to an entry in the Swiss-Prot database, and an xref in an RNA instance pointing to the corresponding RNA sequence in the RefSeq database..
Definition: Utility classes are created when simple slots are insufficient to describe an aspect of an entity or to increase compatibility of this ontology with other standards. The utilityClass class is actually a metaclass and is only present to organize the other helper classes under one class hierarchy; instances of utilityClass should never be created.
Definition: A reference from an instance of a class in this ontology to an object in an external resource. Comment: Instances of the xref class should never be created and more specific classes should be used instead.
This is a key control step in glycolysis |CITS: [79100775]|
In this reaction a phosphoryl group is transferred from the acyl phosphate of 1,3 diphosphoglycerate to ADP thereby forming ATP and 3-phosphoglycerate.|CITS:[90336971]|
Dihydroxyacetone phosphate is also called glycerone phosphate. Of the total aldolase activity in cell-free extracts of E.coli grown on pyruvate and lactate, approx. 60 % was accounted for by aldolase 1. On the other hand, E.coli grown on glucose showed no aldolase 1 activity but had an increased aldolase 2 activity. |CITS: [73229139]| During growth with CO2 as a carbon source, only class I aldolase is produced but when acetate replaces CO2 the class II aldolase is made. Similarly, in E.coli the putative class I aldolase is only synthesized during growth on C3 compounds and not on glucose, implying that a class I aldolase is preferred for gluconeogenesis |CITS:[73229139]|
FRUCTOSE-1,6-BISPHOSPHATE TRIOSEPHOSPHATE-LYASE
Pyruvate kinase I is strongly activated by fructose 1,6 bisphosphate and shows sigmoid kinetics with respect to the substrate phophoenolpyruvate. The dependences of the reaction rate on the concentrations of phosphoenolpyruvate, Mg+2, and Mn+2 are sigmoid. These dependences become hyperbolic on addition of fructose 1,6 bisphosphate. The dependences of the reaction rate on the concentration of ADP are always hyperbolic. The catalytic active complex of E. coli pyruvate kinase is formed by only one conformational state of the enzyme, state R1. This state binds randomly the Mg+2 free ligands ADP or phosphoenolpyruvate. Thereafter, the active enzyme complex is formed by binding Mg+2-PEP or Mg+2ADP respectively. State R2 of coli pyruvate kinase binds randomly ADP and Mg+2. It is the only state in which Mg+2 can bind to the free enzyme. Mg+2 is not necesary for the binding of ADP, PEP an ATP. Mg+2 can inhibit either by binding to the state R2 or by lowering the concentration of Mg+2, free ADP and PEP through complex formation. ATP inhibits by virtue of three effects: increase in ionic strength, complex-formation with Mg+2 when this metal ion acts as an activator and binding to the state R3. However when conditions are such that Mg+2 is an inhibitor, then ATP is expected to activate because of complex formation with Mg+2. In general, one can say that the ligands Mg+2 and ATP cannot be classified as inhibitors or activators because their regulatory effect on the reaction rate depends on the concentration of the other ligands.|CITS:[81159972]| By addition of fructose-1,6-bisphosphate the sigmoid kinetics with respect to phosphoenolpyruvate and Mg+2 is abolished and the activity of the enzyme is described by classical saturation kinetics. This is explained by exclusive binding of fructose 1,6 bisphosphate at an allosteric site of the conformational state that forms the active complex. Ca+2 is an activator of the enzyme at low Mg+2 and Ca+2 concentrations; otherwise it is an inhibitor. These effects can be understood by assuming that Ca+2 has the same binding properties as Mg+2, although it does not allow a catalytic turnover.|CITS:[83282602]| The enzyme requires both bivalent and monovalent cations. |CITS: [90336973]|
Pyruvate kinase II displays only limited cooperativity amoung phosphoenolpyruvate binding sites and is allosterically activated by AMP and several sugar phosphates |CITS:[91315755]| The enzyme requires both bivalent and monovalent cations. |CITS: [90336973]|
E. coli contains three phosphoglycerate mutases. Two are 2,3-bisphosphoglyerate-dependent enzymes, encoded by the gpmA and gpmB genes. The third is a 2,3-bisphosphoglyerate-independent enzyme encoded by the pgmI gene. |CITS: [99364512]|
The E.coli sequence contains a certain number of amino acids which are conserved in all GAPDHs so far sequenced and which are postulated to be directly implicated in the NAD+ binding or in the catalysis mechanism. |CITS:[85257641]| There appear to be only two active sites per molecule.|CITS:[79255500]| NAD required for the phosphorylation as well as the oxidation |CITS:[79255500]|
glyceraldehyde 3-phosphate dehydrogenase-A complex
90% of the activity present in the wild type strain is pfk-1. |CITS: [83294514]| The enzyme shows cooperative kinetics with the substrate fructose-6-phosphate but not with the other substrate ATP. |CITS: [85203917]| The reverse reaction does not participate in gluconeogenesis: fdp phosphatase mutants are deficient in gluconeogenesis.|CITS: [78194149]| Studies on phosphfructokinase-1 include subunit structure |CITS:[91255189]|, ligand binding |CITS: [91355204]| and pH dependence |CITS: [91255189]|. The allosteric properties of phosphofructokinase-1 are due in part to ligand binding and in part to the kinetics of the reaction. |CITS: [92144584]|
2-phospho-D-glycerate phosphotransferase
The structure of Pgk determined crystallographically is best described as an open bi-lobal molecule. The active site of the enzyme lies deep in the cleft formed between the two lobes.|CITS:[90336971]| When purified enzymes were employed there was absolute dependence upon the respective substrates of the glycolytic pathway. There was no activity unless ATP and glycerate-3-P were both included.|CITS:[71230170]|
Pfk-2 is somewhat sensitive to inhibition by fructose-1,6-diphosphate and ATP. Pfk-2,unlike pfk-1, does not show cooperative interaction with fructose-6-phosphate, inhibition by PEP or activation by ADP. |CITS:[84262485]| MgATP is an inhibitor of pfk-2 and it provokes the tetramerization of the dimeric native enzyme.|CITS: [85289307],[88292964]| Its normal function is not known and in strains with pfk-1, pfkB may be deleted without apparent effect. |CITS: [83294514]| However in the absence of pfk-1, slow growth on sugars depends on pfk-2. Its loss causes complete inability to grow. |CITS: [84262485]| The distribution of the two phosphofructokinases is variable among enterobacteria and also among E.coli strains |CITS: [82027179]|
When E. coli K-12 is grown on C-3 carbon sources both classes of aldolase are present. However the Class I enzyme is present only under these conditions. Therefore it is likely that the Class I enzyme is involved in gluconeogenesis and the class II enzyme in glycolysis. |CITS: [81000551]| The class I enzymes function by imine formation between the substrate and a catalytically essential lysine residue in the active site, which acts to stabilize the intermediate carbanion. |CITS:[89193446]| They form a Schiff base betwen the E-amino group of a specific lysine residue in the active site and the carbonyl group of the substrate. This imine may be reduced by borohydride which therefore irreversibly inhibits class 1 aldolases in the presence of substrate. |CITS:[73229139]| The enzyme's activity was unaffected by EDTA, but it was inhibited by borohydride reduction in the presence of Fru-1,6-P2 or dihydroxyacetone phosphate. Like mammalian aldolases, it cleaved fructose 1-phosphate, albeit slowly and had a low Km for Fru-1,6-P2. Its fructose 1,6 bisphosphate cleavage activity was greatly enhanced by citrate, PEP, 2-oxoglutarate and sn-glycerol 3-phosphate. Aldolase I is very efficient at Fru-1,6-P2 cleavage when fully activated. Only a limited range of metabolites has been tested as possible activators. In contrast, its fructose 1-phosphate cleavage activity was unaffected by these compounds. The enhancement exhibited a strong dependence on pH. These novel kinetic properties do not seem to be shared by any other fructose 1,6 bisphosphate aldolase. In view of its unusual properties, it is unlikely that aldolase I from E.coli is closely related to the class-1 aldolases that have been detected in several other prokaryotes, or to the typical class I enzymes from eukaryote. |CITS: [78165652]|
The amino acid sequence around the active site is perfectly conserved in all known triose phosphate isomerases and can be used as a signature pattern for this type of enzyme.|CITS: [Prosite]|
Class II enzymes utilize a divalent metal ion to act as the electron sink at the active site in what appears to be an otherwise similar catalytic mechanism to Class I. |CITS: [89193446]| The metal ion in the active site varies, but several metals including zinc, cobalt, iron, nickel and manganese can form an active metallo-protein complex |CITS: [73229139]| In Crookes strain of E. coli it was found that the kinetic behavior is not typical of a class-II aldolase; the enzyme has no requirement for thiol compounds either for stability or activity, added K+ ions have no effect, and the high pH optimum of 9 is unusual for a class II enzyme. |CITS: [78165651]| Aldolase II is relatively insensitive to compounds that react with thiol groups.|CITS: [78165651]| It is strongly inhibited by metal-chelating agents and is reactivated by bivalent metal ions.|CITS: [73229139]| When E. coli K-12 is grown on C-3 carbon sources both classes of aldolase are present. However the Class I enzyme is present only under these conditions. Therefore the Class I enzyme is most likely involved in gluconeogenesis and the Class II enzyme with glycolysis. |CITS: [81000551]|
fructose-1,6-bisphosphate triosephosphate lyase
2-deoxyglucose-6-p is a known inhibitor in mammalian systems. E.coli cells with mutated pgi gene apparently utilize glucose primarily by the pentose phosphate pathway and to a lesser extent by the Entner-Duodoroff pathway. |CITS:[89364675]|
E. coli contains three phosphoglycerate mutases. Two are 2,3-bisphosphoglycerate-dependent enzymes, encoded by the gpmA and gpmB genes. The third is a 2,3-bisphosphoglycerate-independent enzyme encoded by the pgmI gene. The two cofactor-dependent enzymes are similar in sequence while the cofactor-independent enzyme is unrelated. The cofactor-dependent enzymes have ten times higher specific activity compared to the cofactor-independent enzyme. |CITS: [99364512]|
phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent
phosphoglycerate mutase, BPG-independent
phosphoglycerate mutase, cofactor independent
2-phospho-D glycerate phosphotransferase
There are two active sites per active dimer. Functionally there are many similarities between E. coli enolase and other enolases studied. Thus the dependence on Mg for activity and the inhibition by fluoride in the presence of phosphate are quantitatively very similar for all enolases. Other catalytic parameters are also similar but minor quantitative distinctions indicate that E. coli enolase is more closely related to yeast enolase than to enolases from vertebrate muscle. The pH optimum of 8.1 is significantly higher than that for vertebrate enolases and even somewhat above that of yeast and plant enolases. |CITS:[72060411]|
<atom id="K+-atom1" elementType="K" x2="-1.0" y2="-1.0" formalCharge="1"/> <formula concise="K 1" formalCharge="1"/> 39.098 [K+1]
<atom id="PYRUVATE-atom1" elementType="C" x2="0.36301" y2="-0.2363"/> <atom id="PYRUVATE-atom2" elementType="C" x2="-1.0" y2="-0.2774"/> <atom id="PYRUVATE-atom3" elementType="O" x2="-0.34247" y2="0.87329"/> <atom id="PYRUVATE-atom4" elementType="C" x2="-0.34247" y2="0.10959"/> <atom id="PYRUVATE-atom5" elementType="O" x2="0.36301" y2="-1.0"/> <atom id="PYRUVATE-atom6" elementType="O" x2="0.99658" y2="0.18836"/> <bond id="PYRUVATE-bond1" atomRefs="PYRUVATE-atom6 PYRUVATE-atom1" order="1"/> <bond id="PYRUVATE-bond2" atomRefs="PYRUVATE-atom5 PYRUVATE-atom1" order="2"/> <bond id="PYRUVATE-bond3" atomRefs="PYRUVATE-atom4 PYRUVATE-atom1" order="1"/> <bond id="PYRUVATE-bond4" atomRefs="PYRUVATE-atom3 PYRUVATE-atom4" order="2"/> <bond id="PYRUVATE-bond5" atomRefs="PYRUVATE-atom2 PYRUVATE-atom4" order="1"/> <formula concise="C 3 H 4 O 3" formalCharge="0"/> 88.063 C(=O)(O)C(=O)C
<atom id="CA+2-atom1" elementType="CA" x2="-1.0" y2="-1.0" formalCharge="2"/> <formula concise="CA 1" formalCharge="2"/> 40.08 [Ca+2]
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atomRefs="SUC-COA-atom51 SUC-COA-atom5" order="A"/> <bond id="SUC-COA-bond12" atomRefs="SUC-COA-atom50 SUC-COA-atom33" order="1"/> <bond id="SUC-COA-bond13" atomRefs="SUC-COA-atom49 SUC-COA-atom53" order="1"/> <bond id="SUC-COA-bond14" atomRefs="SUC-COA-atom27 SUC-COA-atom48" order="A"/> <bond id="SUC-COA-bond15" atomRefs="SUC-COA-atom47 SUC-COA-atom43" order="1"/> <bond id="SUC-COA-bond16" atomRefs="SUC-COA-atom46 SUC-COA-atom55" order="1"/> <bond id="SUC-COA-bond17" atomRefs="SUC-COA-atom45 SUC-COA-atom10" order="A"/> <bond id="SUC-COA-bond18" atomRefs="SUC-COA-atom39 SUC-COA-atom45" order="A"/> <bond id="SUC-COA-bond19" atomRefs="SUC-COA-atom44 SUC-COA-atom52" order="1"/> <bond id="SUC-COA-bond20" atomRefs="SUC-COA-atom43 SUC-COA-atom54" order="1"/> <bond id="SUC-COA-bond21" atomRefs="SUC-COA-atom42 SUC-COA-atom13" order="1"/> <bond id="SUC-COA-bond22" atomRefs="SUC-COA-atom41 SUC-COA-atom18" order="2"/> <bond id="SUC-COA-bond23" atomRefs="SUC-COA-atom40 SUC-COA-atom16" order="1"/> <bond id="SUC-COA-bond24" atomRefs="SUC-COA-atom48 SUC-COA-atom39" order="A"/> <bond id="SUC-COA-bond25" atomRefs="SUC-COA-atom38 SUC-COA-atom20" order="1"/> <bond id="SUC-COA-bond26" atomRefs="SUC-COA-atom37 SUC-COA-atom40" order="1"/> <bond id="SUC-COA-bond27" atomRefs="SUC-COA-atom36 SUC-COA-atom37" order="1"/> <bond id="SUC-COA-bond28" atomRefs="SUC-COA-atom35 SUC-COA-atom7" order="1"/> <bond id="SUC-COA-bond29" atomRefs="SUC-COA-atom34 SUC-COA-atom50" order="1"/> <bond id="SUC-COA-bond30" atomRefs="SUC-COA-atom33 SUC-COA-atom47" order="1"/> <bond id="SUC-COA-bond31" atomRefs="SUC-COA-atom32 SUC-COA-atom17" order="1"/> <bond id="SUC-COA-bond32" atomRefs="SUC-COA-atom31 SUC-COA-atom57" order="1"/> <bond id="SUC-COA-bond33" atomRefs="SUC-COA-atom30 SUC-COA-atom50" order="2"/> <bond id="SUC-COA-bond34" atomRefs="SUC-COA-atom28 SUC-COA-atom26" order="1"/> <bond id="SUC-COA-bond35" atomRefs="SUC-COA-atom26 SUC-COA-atom32" order="1"/> <bond id="SUC-COA-bond36" atomRefs="SUC-COA-atom25 SUC-COA-atom47" order="1"/> <bond id="SUC-COA-bond37" atomRefs="SUC-COA-atom39 SUC-COA-atom24" order="A"/> <bond id="SUC-COA-bond38" atomRefs="SUC-COA-atom24 SUC-COA-atom12" order="A"/> <bond id="SUC-COA-bond39" atomRefs="SUC-COA-atom23 SUC-COA-atom3" order="1"/> <bond id="SUC-COA-bond40" atomRefs="SUC-COA-atom22 SUC-COA-atom44" order="1"/> <bond id="SUC-COA-bond41" atomRefs="SUC-COA-atom21 SUC-COA-atom47" order="2"/> <bond id="SUC-COA-bond42" atomRefs="SUC-COA-atom20 SUC-COA-atom42" order="1"/> <bond id="SUC-COA-bond43" atomRefs="SUC-COA-atom19 SUC-COA-atom20" order="2"/> <bond id="SUC-COA-bond44" atomRefs="SUC-COA-atom18 SUC-COA-atom36" order="1"/> <bond id="SUC-COA-bond45" atomRefs="SUC-COA-atom17 SUC-COA-atom50" order="1"/> <bond id="SUC-COA-bond46" atomRefs="SUC-COA-atom16 SUC-COA-atom22" order="1"/> <bond id="SUC-COA-bond47" atomRefs="SUC-COA-atom15 SUC-COA-atom22" order="2"/> <bond id="SUC-COA-bond48" atomRefs="SUC-COA-atom14 SUC-COA-atom1" order="1"/> <bond id="SUC-COA-bond49" atomRefs="SUC-COA-atom13 SUC-COA-atom18" order="1"/> <bond id="SUC-COA-bond50" atomRefs="SUC-COA-atom12 SUC-COA-atom51" order="A"/> <bond id="SUC-COA-bond51" atomRefs="SUC-COA-atom11 SUC-COA-atom7" order="1"/> <bond id="SUC-COA-bond52" atomRefs="SUC-COA-atom10 SUC-COA-atom27" order="A"/> <bond id="SUC-COA-bond53" atomRefs="SUC-COA-atom9 SUC-COA-atom3" order="1"/> <bond id="SUC-COA-bond54" atomRefs="SUC-COA-atom8 SUC-COA-atom53" order="1"/> <bond id="SUC-COA-bond55" atomRefs="SUC-COA-atom7 SUC-COA-atom29" order="1"/> <bond id="SUC-COA-bond56" atomRefs="SUC-COA-atom6 SUC-COA-atom8" order="2"/> <bond id="SUC-COA-bond57" atomRefs="SUC-COA-atom5 SUC-COA-atom48" order="A"/> <bond id="SUC-COA-bond58" atomRefs="SUC-COA-atom4 SUC-COA-atom26" order="1"/> <bond id="SUC-COA-bond59" atomRefs="SUC-COA-atom2 SUC-COA-atom8" order="1"/> <bond id="SUC-COA-bond60" atomRefs="SUC-COA-atom1 SUC-COA-atom27" order="1"/> <bond id="SUC-COA-bond61" atomRefs="SUC-COA-atom1 SUC-COA-atom3" order="1"/> <formula concise="C 25 H 40 N 7 O 19 P 3 S 1" formalCharge="0"/> 867.608 [CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH]([CH](O)3)OP(O)(=O)O)COP(=O)(O)OP(=O)(O)OCC(C)(C)C(O)C(=O)NCCC(=O)NCCSC(=O)CCC(O)=O) Coenzyme A, S-(hydrogen butanedioate)
<atom id="AMP-atom1" elementType="O" x2="0.45706" y2="-1.0"/> <atom id="AMP-atom2" elementType="O" x2="0.25153" y2="0.00307"/> <atom id="AMP-atom3" elementType="C" x2="0.41718" y2="-0.2362"/> <atom id="AMP-atom4" elementType="N" x2="-1.0" y2="-0.25767"/> <atom id="AMP-atom5" elementType="N" x2="-0.15951" y2="-0.25767"/> <atom id="AMP-atom6" elementType="H" x2="0.56442" y2="-0.32822"/> <atom id="AMP-atom7" elementType="N" x2="-0.16258" y2="0.2454"/> <atom id="AMP-atom8" elementType="C" x2="0.70859" y2="0.15031"/> <atom id="AMP-atom9" elementType="C" x2="-0.57055" y2="-0.0184"/> <atom id="AMP-atom10" elementType="C" x2="0.42025" y2="0.2454"/> <atom id="AMP-atom11" elementType="C" x2="0.70859" y2="-0.14417"/> <atom id="AMP-atom12" elementType="N" x2="-0.57669" y2="-0.49693"/> <atom id="AMP-atom13" elementType="O" x2="0.09509" y2="-0.58282"/> <atom id="AMP-atom14" elementType="C" x2="-0.41718" y2="0.41104"/> <atom id="AMP-atom15" elementType="O" x2="0.99693" y2="-0.14417"/> <atom id="AMP-atom16" elementType="O" x2="0.98466" y2="0.23006"/> <atom id="AMP-atom17" elementType="C" x2="-0.30061" y2="-0.0184"/> <atom id="AMP-atom18" elementType="C" x2="-0.71166" y2="-0.25767"/> <atom id="AMP-atom19" elementType="P" x2="0.26994" y2="-0.78221"/> <atom id="AMP-atom20" elementType="N" x2="-0.67485" y2="0.22086"/> <atom id="AMP-atom21" elementType="H" x2="0.42025" y2="0.41718"/> <atom id="AMP-atom22" elementType="C" x2="-0.29755" y2="-0.49693"/> <atom id="AMP-atom23" elementType="O" x2="0.5" y2="-0.60736"/> <atom id="AMP-atom24" elementType="C" x2="0.09509" y2="-0.33742"/> <atom id="AMP-atom25" elementType="O" x2="0.02761" y2="-0.93865"/> <bond id="AMP-bond1" atomRefs="AMP-atom25 AMP-atom19" order="1"/> <bond id="AMP-bond2" atomRefs="AMP-atom23 AMP-atom19" order="2"/> <bond id="AMP-bond3" atomRefs="AMP-atom22 AMP-atom5" order="A"/> <bond id="AMP-bond4" atomRefs="AMP-atom9 AMP-atom20" order="A"/> <bond id="AMP-bond5" atomRefs="AMP-atom20 AMP-atom14" order="A"/> <bond id="AMP-bond6" atomRefs="AMP-atom19 AMP-atom13" order="1"/> <bond id="AMP-bond7" atomRefs="AMP-atom18 AMP-atom12" order="A"/> <bond id="AMP-bond8" atomRefs="AMP-atom9 AMP-atom18" order="A"/> <bond id="AMP-bond9" atomRefs="AMP-atom7 AMP-atom17" order="A"/> <bond id="AMP-bond10" atomRefs="AMP-atom14 AMP-atom7" order="A"/> <bond id="AMP-bond11" atomRefs="AMP-atom13 AMP-atom24" order="1"/> <bond id="AMP-bond12" atomRefs="AMP-atom12 AMP-atom22" order="A"/> <bond id="AMP-bond13" atomRefs="AMP-atom11 AMP-atom15" order="1"/> <bond id="AMP-bond14" atomRefs="AMP-atom11 AMP-atom8" order="1"/> <bond id="AMP-bond15" atomRefs="AMP-atom10 AMP-atom21" order="1"/> <bond id="AMP-bond16" atomRefs="AMP-atom10 AMP-atom7" order="1"/> <bond id="AMP-bond17" atomRefs="AMP-atom17 AMP-atom9" order="A"/> <bond id="AMP-bond18" atomRefs="AMP-atom8 AMP-atom16" order="1"/> <bond id="AMP-bond19" atomRefs="AMP-atom8 AMP-atom10" order="1"/> <bond id="AMP-bond20" atomRefs="AMP-atom5 AMP-atom17" order="A"/> <bond id="AMP-bond21" atomRefs="AMP-atom4 AMP-atom18" order="1"/> <bond id="AMP-bond22" atomRefs="AMP-atom3 AMP-atom11" order="1"/> <bond id="AMP-bond23" atomRefs="AMP-atom3 AMP-atom6" order="1"/> <bond id="AMP-bond24" atomRefs="AMP-atom3 AMP-atom24" order="1"/> <bond id="AMP-bond25" atomRefs="AMP-atom3 AMP-atom2" order="1"/> <bond id="AMP-bond26" atomRefs="AMP-atom2 AMP-atom10" order="1"/> <bond id="AMP-bond27" atomRefs="AMP-atom1 AMP-atom19" order="1"/> <formula concise="C 10 H 14 N 5 O 7 P 1" formalCharge="-2"/> 347.224 [CH]1(O[CH](C(O)C(O)1)COP(=O)(O)O)n2(c3(c(nc2)c(N)ncn3))
<atom id="Pi-atom1" elementType="P" x2="-0.00166" y2="-0.00166"/> <atom id="Pi-atom2" elementType="O" x2="0.99667" y2="-0.00166" formalCharge="-1"/> <atom id="Pi-atom3" elementType="O" x2="-0.00166" y2="0.99667" formalCharge="-1"/> <atom id="Pi-atom4" elementType="O" x2="-0.00166" y2="-1.0" formalCharge="-1"/> <atom id="Pi-atom5" elementType="O" x2="-1.0" y2="-0.00166"/> <bond id="Pi-bond1" atomRefs="Pi-atom5 Pi-atom1" order="2"/> <bond id="Pi-bond2" atomRefs="Pi-atom4 Pi-atom1" order="1"/> <bond id="Pi-bond3" atomRefs="Pi-atom3 Pi-atom1" order="1"/> <bond id="Pi-bond4" atomRefs="Pi-atom2 Pi-atom1" order="1"/> <formula concise="O 4 P 1" formalCharge="-3"/> 94.971 P([O-1])([O-1])(=O)[O-1]
<atom id="NADH-atom1" elementType="C" x2="0.34285715" y2="-0.7542857"/> <atom id="NADH-atom2" elementType="C" x2="0.92" y2="-0.45142856"/> <atom id="NADH-atom3" elementType="H" x2="0.37142858" y2="-0.89428574"/> <atom id="NADH-atom4" elementType="O" x2="0.08285714" y2="-0.64"/> <atom id="NADH-atom5" elementType="O" x2="0.08285714" y2="-0.8657143"/> <atom id="NADH-atom6" elementType="C" x2="0.42857143" y2="-0.93142855"/> <atom id="NADH-atom7" elementType="C" x2="-0.5914286" y2="-0.36"/> <atom id="NADH-atom8" elementType="C" x2="-0.78571427" y2="-0.4342857"/> <atom id="NADH-atom9" elementType="H" x2="-0.48857144" y2="-0.70285714"/> <atom id="NADH-atom10" elementType="H" x2="0.7" y2="-0.34285715"/> <atom id="NADH-atom11" elementType="O" x2="0.42857143" y2="-1.0"/> <atom id="NADH-atom12" elementType="C" x2="0.52" y2="-0.46285716"/> <atom id="NADH-atom13" elementType="C" x2="-1.0" y2="-0.4342857"/> <atom id="NADH-atom14" elementType="H" x2="0.42857143" y2="-0.86285716"/> <atom id="NADH-atom15" elementType="H" x2="-0.68" y2="-0.7542857"/> <atom id="NADH-atom16" elementType="H" x2="0.6028572" y2="-0.34571427"/> <atom id="NADH-atom17" elementType="C" x2="-0.42285714" y2="-0.68285716"/> <atom id="NADH-atom18" elementType="C" x2="0.7714286" y2="-0.45142856"/> <atom id="NADH-atom19" elementType="H" x2="0.6457143" y2="-0.89428574"/> <atom id="NADH-atom20" elementType="O" x2="-0.5542857" y2="-0.61142856"/> <atom id="NADH-atom21" elementType="C" x2="0.6457143" y2="-0.82857144"/> <atom id="NADH-atom22" elementType="O" x2="-0.48857144" y2="-0.8428571"/> <atom id="NADH-atom23" elementType="C" x2="0.37142858" y2="-0.82857144"/> <atom id="NADH-atom24" elementType="C" x2="0.52" y2="-0.6085714"/> <atom id="NADH-atom25" elementType="C" x2="-0.48857144" y2="-0.77428573"/> <atom id="NADH-atom26" elementType="C" x2="-0.61714286" y2="-0.77428573"/> <atom id="NADH-atom27" elementType="O" x2="0.5" y2="-0.7457143"/> <atom id="NADH-atom28" elementType="N" x2="-0.8971428" y2="-0.13142857"/> <atom id="NADH-atom29" elementType="O" x2="0.21428572" y2="-0.7542857"/> <atom id="NADH-atom30" elementType="O" x2="-0.17714286" y2="-0.64"/> <atom id="NADH-atom31" elementType="N" x2="-1.0" y2="-0.31142858"/> <atom id="NADH-atom32" elementType="N" x2="-0.68" y2="-0.48285714"/> <atom id="NADH-atom33" elementType="N" x2="0.9942857" y2="-0.5342857"/> <atom id="NADH-atom34" elementType="C" x2="0.7714286" y2="-0.6085714"/> <atom id="NADH-atom35" elementType="C" x2="-0.78571427" y2="-0.31142858"/> <atom id="NADH-atom36" elementType="H" x2="0.5714286" y2="-0.86285716"/> <atom id="NADH-atom37" elementType="P" x2="0.08285714" y2="-0.7542857"/> <atom id="NADH-atom38" elementType="O" x2="-0.61714286" y2="-0.8428571"/> <atom id="NADH-atom39" elementType="N" x2="-0.68" y2="-0.25714287"/> <atom id="NADH-atom40" elementType="P" x2="-0.17714286" y2="-0.7542857"/> <atom id="NADH-atom41" elementType="C" x2="-0.68" y2="-0.68285716"/> <atom id="NADH-atom42" elementType="N" x2="0.6457143" y2="-0.67714286"/> <atom id="NADH-atom43" elementType="H" x2="-0.61714286" y2="-0.70285714"/> <atom id="NADH-atom44" elementType="O" x2="0.99714285" y2="-0.37142858"/> <atom id="NADH-atom45" elementType="N" x2="-0.8971428" y2="-0.48857144"/> <atom id="NADH-atom46" elementType="C" x2="-0.36857143" y2="-0.7657143"/> <atom id="NADH-atom47" elementType="O" x2="0.5714286" y2="-1.0"/> <atom id="NADH-atom48" elementType="O" x2="-0.17714286" y2="-0.8657143"/> <atom id="NADH-atom49" elementType="C" x2="-0.8971428" y2="-0.24857143"/> <atom id="NADH-atom50" elementType="O" x2="-0.2742857" y2="-0.7542857"/> <atom id="NADH-atom51" elementType="H" x2="-0.42285714" y2="-0.61714286"/> <atom id="NADH-atom52" elementType="O" x2="-0.042857144" y2="-0.7542857"/> <atom id="NADH-atom53" elementType="C" x2="0.5714286" y2="-0.93142855"/> <atom id="NADH-atom54" elementType="C" x2="0.6542857" y2="-0.39142856"/> <bond id="NADH-bond1" atomRefs="NADH-atom54 NADH-atom18" order="1"/> <bond id="NADH-bond2" atomRefs="NADH-atom53 NADH-atom6" order="1"/> <bond id="NADH-bond3" atomRefs="NADH-atom52 NADH-atom40" order="1"/> <bond id="NADH-bond4" atomRefs="NADH-atom51 NADH-atom17" order="1"/> <bond id="NADH-bond5" atomRefs="NADH-atom50 NADH-atom46" order="1"/> <bond id="NADH-bond6" atomRefs="NADH-atom49 NADH-atom31" order="A"/> <bond id="NADH-bond7" atomRefs="NADH-atom48 NADH-atom40" order="1"/> <bond id="NADH-bond8" atomRefs="NADH-atom47 NADH-atom53" order="1"/> <bond id="NADH-bond9" atomRefs="NADH-atom46 NADH-atom17" order="1"/> <bond id="NADH-bond10" atomRefs="NADH-atom45 NADH-atom8" order="A"/> <bond id="NADH-bond11" atomRefs="NADH-atom44 NADH-atom2" order="2"/> <bond id="NADH-bond12" atomRefs="NADH-atom43 NADH-atom26" order="1"/> <bond id="NADH-bond13" atomRefs="NADH-atom42 NADH-atom21" order="1"/> <bond id="NADH-bond14" atomRefs="NADH-atom42 NADH-atom24" order="1"/> <bond id="NADH-bond15" atomRefs="NADH-atom41 NADH-atom32" order="1"/> <bond id="NADH-bond16" atomRefs="NADH-atom41 NADH-atom26" order="1"/> <bond id="NADH-bond17" atomRefs="NADH-atom40 NADH-atom50" order="1"/> <bond id="NADH-bond18" atomRefs="NADH-atom39 NADH-atom35" order="A"/> <bond id="NADH-bond19" atomRefs="NADH-atom38 NADH-atom26" order="1"/> <bond id="NADH-bond20" atomRefs="NADH-atom37 NADH-atom52" order="1"/> <bond id="NADH-bond21" atomRefs="NADH-atom36 NADH-atom53" order="1"/> <bond id="NADH-bond22" atomRefs="NADH-atom35 NADH-atom49" order="A"/> <bond id="NADH-bond23" atomRefs="NADH-atom35 NADH-atom8" order="A"/> <bond id="NADH-bond24" atomRefs="NADH-atom34 NADH-atom42" order="1"/> <bond id="NADH-bond25" atomRefs="NADH-atom33 NADH-atom2" order="1"/> <bond id="NADH-bond26" atomRefs="NADH-atom32 NADH-atom7" order="A"/> <bond id="NADH-bond27" atomRefs="NADH-atom31 NADH-atom13" order="A"/> <bond id="NADH-bond28" atomRefs="NADH-atom30 NADH-atom40" order="2"/> <bond id="NADH-bond29" atomRefs="NADH-atom29 NADH-atom37" order="1"/> <bond id="NADH-bond30" atomRefs="NADH-atom28 NADH-atom49" order="1"/> <bond id="NADH-bond31" atomRefs="NADH-atom27 NADH-atom23" order="1"/> <bond id="NADH-bond32" atomRefs="NADH-atom25 NADH-atom26" order="1"/> <bond id="NADH-bond33" atomRefs="NADH-atom23 NADH-atom1" order="1"/> <bond id="NADH-bond34" atomRefs="NADH-atom23 NADH-atom6" order="1"/> <bond id="NADH-bond35" atomRefs="NADH-atom22 NADH-atom25" order="1"/> <bond id="NADH-bond36" atomRefs="NADH-atom21 NADH-atom27" order="1"/> <bond id="NADH-bond37" atomRefs="NADH-atom21 NADH-atom53" order="1"/> <bond id="NADH-bond38" atomRefs="NADH-atom20 NADH-atom41" order="1"/> <bond id="NADH-bond39" atomRefs="NADH-atom19 NADH-atom21" order="1"/> <bond id="NADH-bond40" atomRefs="NADH-atom18 NADH-atom34" order="2"/> <bond id="NADH-bond41" atomRefs="NADH-atom17 NADH-atom20" order="1"/> <bond id="NADH-bond42" atomRefs="NADH-atom17 NADH-atom25" order="1"/> <bond id="NADH-bond43" atomRefs="NADH-atom16 NADH-atom54" order="1"/> <bond id="NADH-bond44" atomRefs="NADH-atom15 NADH-atom41" order="1"/> <bond id="NADH-bond45" atomRefs="NADH-atom14 NADH-atom6" order="1"/> <bond id="NADH-bond46" atomRefs="NADH-atom13 NADH-atom45" order="A"/> <bond id="NADH-bond47" atomRefs="NADH-atom12 NADH-atom24" order="2"/> <bond id="NADH-bond48" atomRefs="NADH-atom12 NADH-atom54" order="1"/> <bond id="NADH-bond49" atomRefs="NADH-atom11 NADH-atom6" order="1"/> <bond id="NADH-bond50" atomRefs="NADH-atom10 NADH-atom54" order="1"/> <bond id="NADH-bond51" atomRefs="NADH-atom9 NADH-atom25" order="1"/> <bond id="NADH-bond52" atomRefs="NADH-atom8 NADH-atom32" order="A"/> <bond id="NADH-bond53" atomRefs="NADH-atom7 NADH-atom39" order="A"/> <bond id="NADH-bond54" atomRefs="NADH-atom5 NADH-atom37" order="1"/> <bond id="NADH-bond55" atomRefs="NADH-atom4 NADH-atom37" order="2"/> <bond id="NADH-bond56" atomRefs="NADH-atom3 NADH-atom23" order="1"/> <bond id="NADH-bond57" atomRefs="NADH-atom2 NADH-atom18" order="1"/> <bond id="NADH-bond58" atomRefs="NADH-atom1 NADH-atom29" order="1"/> <formula concise="C 21 H 29 N 7 O 14 P 2" formalCharge="0"/> 665.446 C([CH]1(O[CH]([CH](O)[CH]1O)N2(C=C(C(=O)N)[CH2]C=C2)))OP(=O)(O)OP(=O)(O)OC[CH]3(O[CH]([CH](O)[CH](O)3)n4(c5(c(nc4)c(N)ncn5)))
<atom id="GAP-atom1" elementType="C" x2="-1.0" y2="-0.54088"/> <atom id="GAP-atom2" elementType="P" x2="-0.1478" y2="0.53774"/> <atom id="GAP-atom3" elementType="O" x2="-0.13836" y2="-0.2044"/> <atom id="GAP-atom4" elementType="O" x2="0.31132" y2="0.53774"/> <atom id="GAP-atom5" elementType="O" x2="-0.1478" y2="0.07862"/> <atom id="GAP-atom6" elementType="O" x2="-1.0" y2="-1.0"/> <atom id="GAP-atom7" elementType="O" x2="-0.1478" y2="0.99686"/> <atom id="GAP-atom8" elementType="C" x2="-1.0" y2="0.1761"/> <atom id="GAP-atom9" elementType="O" x2="-0.59748" y2="0.53774"/> <atom id="GAP-atom10" elementType="C" x2="-0.59748" y2="-0.2044"/> <bond id="GAP-bond1" atomRefs="GAP-atom10 GAP-atom3" order="1"/> <bond id="GAP-bond2" atomRefs="GAP-atom10 GAP-atom8" order="1"/> <bond id="GAP-bond3" atomRefs="GAP-atom9 GAP-atom2" order="1"/> <bond id="GAP-bond4" atomRefs="GAP-atom8 GAP-atom9" order="1"/> <bond id="GAP-bond5" atomRefs="GAP-atom6 GAP-atom1" order="2"/> <bond id="GAP-bond6" atomRefs="GAP-atom2 GAP-atom5" order="1"/> <bond id="GAP-bond7" atomRefs="GAP-atom2 GAP-atom7" order="1"/> <bond id="GAP-bond8" atomRefs="GAP-atom2 GAP-atom4" order="2"/> <bond id="GAP-bond9" atomRefs="GAP-atom1 GAP-atom10" order="1"/> <formula concise="C 3 H 7 O 6 P 1" formalCharge="0"/> 170.058 C(=O)C(O)COP(O)(O)=O
<atom id="NAD-atom1" elementType="C" x2="-0.35491604" y2="-0.73141485"/> <atom id="NAD-atom2" elementType="N" x2="0.6834533" y2="-0.64028776" formalCharge="1"/> <atom id="NAD-atom3" elementType="C" x2="-0.7793765" y2="-0.2589928"/> <atom id="NAD-atom4" elementType="N" x2="-0.67146283" y2="-0.41246998"/> <atom id="NAD-atom5" elementType="H" x2="-0.6618705" y2="-0.7050359"/> <atom id="NAD-atom6" elementType="C" x2="0.45803356" y2="-0.9256595"/> <atom id="NAD-atom7" elementType="O" x2="-0.016786575" y2="-0.71702635"/> <atom id="NAD-atom8" elementType="O" x2="0.6139089" y2="-1.0"/> <atom id="NAD-atom9" elementType="O" x2="-0.58752996" y2="-0.7865707"/> <atom id="NAD-atom10" elementType="C" x2="0.6906475" y2="-0.34532374"/> <atom id="NAD-atom11" elementType="C" x2="-1.0" y2="-0.3860911"/> <atom id="NAD-atom12" elementType="O" x2="-0.5467626" y2="-0.5707434"/> <atom id="NAD-atom13" elementType="C" x2="0.37649882" y2="-0.71702635"/> <atom id="NAD-atom14" elementType="P" x2="-0.15347719" y2="-0.71702635"/> <atom id="NAD-atom15" elementType="O" x2="0.24460435" y2="-0.71702635"/> <atom id="NAD-atom16" elementType="C" x2="-0.8920863" y2="-0.1966427"/> <atom id="NAD-atom17" elementType="C" x2="-0.4028777" y2="-0.6522782"/> <atom id="NAD-atom18" elementType="O" x2="-0.15347719" y2="-0.5971223"/> <atom id="NAD-atom19" elementType="O" x2="-0.47961628" y2="-0.7865707"/> <atom id="NAD-atom20" elementType="C" x2="0.6139089" y2="-0.9256595"/> <atom id="NAD-atom21" elementType="N" x2="-0.8920863" y2="-0.076738596"/> <atom id="NAD-atom22" elementType="H" x2="0.6139089" y2="-0.853717"/> <atom id="NAD-atom23" elementType="H" x2="-0.58752996" y2="-0.64028776"/> <atom id="NAD-atom24" elementType="C" x2="-0.5851319" y2="-0.31414866"/> <atom id="NAD-atom25" elementType="H" x2="0.45803356" y2="-0.853717"/> <atom id="NAD-atom26" elementType="C" x2="0.96642685" y2="-0.40527576"/> <atom id="NAD-atom27" elementType="C" x2="-0.67146283" y2="-0.6354916"/> <atom id="NAD-atom28" elementType="C" x2="0.556355" y2="-0.5683453"/> <atom id="NAD-atom29" elementType="H" x2="-0.4028777" y2="-0.5779376"/> <atom id="NAD-atom30" elementType="N" x2="-1.0" y2="-0.2589928"/> <atom id="NAD-atom31" elementType="C" x2="0.6834533" y2="-0.8057554"/> <atom id="NAD-atom32" elementType="C" x2="0.37649882" y2="-0.8057554"/> <atom id="NAD-atom33" elementType="H" x2="0.37649882" y2="-0.8800959"/> <atom id="NAD-atom34" elementType="O" x2="-0.25659472" y2="-0.71702635"/> <atom id="NAD-atom35" elementType="O" x2="-0.15347719" y2="-0.83693045"/> <atom id="NAD-atom36" elementType="O" x2="0.53237414" y2="-0.7505995"/> <atom id="NAD-atom37" elementType="C" x2="-0.58752996" y2="-0.7146283"/> <atom id="NAD-atom38" elementType="C" x2="0.8153478" y2="-0.42206234"/> <atom id="NAD-atom39" elementType="C" x2="0.8153478" y2="-0.5683453"/> <atom id="NAD-atom40" elementType="O" x2="0.45803356" y2="-1.0"/> <atom id="NAD-atom41" elementType="O" x2="0.10791373" y2="-0.83693045" formalCharge="-1"/> <atom id="NAD-atom42" elementType="O" x2="0.96642685" y2="-0.28537166"/> <atom id="NAD-atom43" elementType="P" x2="0.10791373" y2="-0.71702635"/> <atom id="NAD-atom44" elementType="N" x2="-0.8920863" y2="-0.4484412"/> <atom id="NAD-atom45" elementType="C" x2="-0.47961628" y2="-0.7146283"/> <atom id="NAD-atom46" elementType="H" x2="-0.47961628" y2="-0.64028776"/> <atom id="NAD-atom47" elementType="O" x2="0.10791373" y2="-0.5971223"/> <atom id="NAD-atom48" elementType="H" x2="0.6834533" y2="-0.8800959"/> <atom id="NAD-atom49" elementType="C" x2="0.556355" y2="-0.4172662"/> <atom id="NAD-atom50" elementType="N" x2="-0.67146283" y2="-0.20383692"/> <atom id="NAD-atom51" elementType="C" x2="-0.7793765" y2="-0.3860911"/> <atom id="NAD-atom52" elementType="N" x2="0.997602" y2="-0.5203837"/> <bond id="NAD-bond1" atomRefs="NAD-atom52 NAD-atom26" order="1"/> <bond id="NAD-bond2" atomRefs="NAD-atom51 NAD-atom3" order="A"/> <bond id="NAD-bond3" atomRefs="NAD-atom50 NAD-atom24" order="A"/> <bond id="NAD-bond4" atomRefs="NAD-atom49 NAD-atom10" order="A"/> <bond id="NAD-bond5" atomRefs="NAD-atom48 NAD-atom31" order="1"/> <bond id="NAD-bond6" atomRefs="NAD-atom47 NAD-atom43" order="2"/> <bond id="NAD-bond7" atomRefs="NAD-atom46 NAD-atom45" order="1"/> <bond id="NAD-bond8" atomRefs="NAD-atom45 NAD-atom37" order="1"/> <bond id="NAD-bond9" atomRefs="NAD-atom44 NAD-atom51" order="A"/> <bond id="NAD-bond10" atomRefs="NAD-atom43 NAD-atom7" order="1"/> <bond id="NAD-bond11" atomRefs="NAD-atom42 NAD-atom26" order="2"/> <bond id="NAD-bond12" atomRefs="NAD-atom41 NAD-atom43" order="1"/> <bond id="NAD-bond13" atomRefs="NAD-atom40 NAD-atom6" order="1"/> <bond id="NAD-bond14" atomRefs="NAD-atom39 NAD-atom2" order="A"/> <bond id="NAD-bond15" atomRefs="NAD-atom38 NAD-atom39" order="A"/> <bond id="NAD-bond16" atomRefs="NAD-atom36 NAD-atom32" order="1"/> <bond id="NAD-bond17" atomRefs="NAD-atom35 NAD-atom14" order="1"/> <bond id="NAD-bond18" atomRefs="NAD-atom34 NAD-atom1" order="1"/> <bond id="NAD-bond19" atomRefs="NAD-atom33 NAD-atom32" order="1"/> <bond id="NAD-bond20" atomRefs="NAD-atom32 NAD-atom6" order="1"/> <bond id="NAD-bond21" atomRefs="NAD-atom32 NAD-atom13" order="1"/> <bond id="NAD-bond22" atomRefs="NAD-atom31 NAD-atom20" order="1"/> <bond id="NAD-bond23" atomRefs="NAD-atom31 NAD-atom36" order="1"/> <bond id="NAD-bond24" atomRefs="NAD-atom30 NAD-atom11" order="A"/> <bond id="NAD-bond25" atomRefs="NAD-atom29 NAD-atom17" order="1"/> <bond id="NAD-bond26" atomRefs="NAD-atom28 NAD-atom49" order="A"/> <bond id="NAD-bond27" atomRefs="NAD-atom27 NAD-atom37" order="1"/> <bond id="NAD-bond28" atomRefs="NAD-atom27 NAD-atom4" order="1"/> <bond id="NAD-bond29" atomRefs="NAD-atom26 NAD-atom38" order="1"/> <bond id="NAD-bond30" atomRefs="NAD-atom25 NAD-atom6" order="1"/> <bond id="NAD-bond31" atomRefs="NAD-atom24 NAD-atom4" order="A"/> <bond id="NAD-bond32" atomRefs="NAD-atom23 NAD-atom37" order="1"/> <bond id="NAD-bond33" atomRefs="NAD-atom22 NAD-atom20" order="1"/> <bond id="NAD-bond34" atomRefs="NAD-atom21 NAD-atom16" order="1"/> <bond id="NAD-bond35" atomRefs="NAD-atom20 NAD-atom6" order="1"/> <bond id="NAD-bond36" atomRefs="NAD-atom19 NAD-atom45" order="1"/> <bond id="NAD-bond37" atomRefs="NAD-atom18 NAD-atom14" order="2"/> <bond id="NAD-bond38" atomRefs="NAD-atom17 NAD-atom45" order="1"/> <bond id="NAD-bond39" atomRefs="NAD-atom17 NAD-atom12" order="1"/> <bond id="NAD-bond40" atomRefs="NAD-atom16 NAD-atom30" order="A"/> <bond id="NAD-bond41" atomRefs="NAD-atom15 NAD-atom43" order="1"/> <bond id="NAD-bond42" atomRefs="NAD-atom14 NAD-atom34" order="1"/> <bond id="NAD-bond43" atomRefs="NAD-atom13 NAD-atom15" order="1"/> <bond id="NAD-bond44" atomRefs="NAD-atom12 NAD-atom27" order="1"/> <bond id="NAD-bond45" atomRefs="NAD-atom11 NAD-atom44" order="A"/> <bond id="NAD-bond46" atomRefs="NAD-atom10 NAD-atom38" order="A"/> <bond id="NAD-bond47" atomRefs="NAD-atom9 NAD-atom37" order="1"/> <bond id="NAD-bond48" atomRefs="NAD-atom8 NAD-atom20" order="1"/> <bond id="NAD-bond49" atomRefs="NAD-atom7 NAD-atom14" order="1"/> <bond id="NAD-bond50" atomRefs="NAD-atom5 NAD-atom27" order="1"/> <bond id="NAD-bond51" atomRefs="NAD-atom4 NAD-atom51" order="A"/> <bond id="NAD-bond52" atomRefs="NAD-atom3 NAD-atom50" order="A"/> <bond id="NAD-bond53" atomRefs="NAD-atom3 NAD-atom16" order="A"/> <bond id="NAD-bond54" atomRefs="NAD-atom2 NAD-atom31" order="1"/> <bond id="NAD-bond55" atomRefs="NAD-atom2 NAD-atom28" order="A"/> <bond id="NAD-bond56" atomRefs="NAD-atom1 NAD-atom17" order="1"/> <formula concise="C 21 H 27 N 7 O 14 P 2" formalCharge="0"/> 663.43 C([CH]1(O[CH]([CH](O)[CH](O)1)n2(c3(c(nc2)c(N)ncn3))))OP(=O)(O)OP([O-1])(=O)OC[CH]4(O[CH]([CH](O)[CH](O)4)[n+1]5(cc(C(N)=O)ccc5))
<atom id="ADP-atom1" elementType="C" x2="0.6623" y2="-0.17049"/> <atom id="ADP-atom2" elementType="N" x2="0.28197" y2="0.02295"/> <atom id="ADP-atom3" elementType="N" x2="0.46557" y2="-0.26885"/> <atom id="ADP-atom4" elementType="O" x2="-0.77705" y2="-0.78689"/> <atom id="ADP-atom5" elementType="O" x2="-0.36721" y2="-0.34098"/> <atom id="ADP-atom6" elementType="C" x2="0.46557" y2="-0.65902"/> <atom id="ADP-atom7" elementType="C" x2="0.22951" y2="-0.54426"/> <atom id="ADP-atom8" elementType="C" x2="0.87541" y2="-0.61967"/> <atom id="ADP-atom9" elementType="O" x2="-1.0" y2="-0.54426"/> <atom id="ADP-atom10" elementType="O" x2="-0.77705" y2="-0.34098"/> <atom id="ADP-atom11" elementType="O" x2="0.88525" y2="-0.97705"/> <atom id="ADP-atom12" elementType="P" x2="-0.36721" y2="-0.54426"/> <atom id="ADP-atom13" elementType="N" x2="0.46557" y2="0.34426"/> <atom id="ADP-atom14" elementType="N" x2="0.87541" y2="-0.21639"/> <atom id="ADP-atom15" elementType="P" x2="-0.77705" y2="-0.54426"/> <atom id="ADP-atom16" elementType="C" x2="0.99672" y2="-0.04262"/> <atom id="ADP-atom17" elementType="O" x2="0.53115" y2="-1.0"/> <atom id="ADP-atom18" elementType="O" x2="-0.57049" y2="-0.54426"/> <atom id="ADP-atom19" elementType="O" x2="-0.1541" y2="-0.54426"/> <atom id="ADP-atom20" elementType="C" x2="0.46557" y2="0.12131"/> <atom id="ADP-atom21" elementType="O" x2="0.65574" y2="-0.47541"/> <atom id="ADP-atom22" elementType="C" x2="0.6623" y2="0.02295"/> <atom id="ADP-atom23" elementType="C" x2="0.81311" y2="-0.86557"/> <atom id="ADP-atom24" elementType="H" x2="0.39344" y2="-0.77377"/> <atom id="ADP-atom25" elementType="N" x2="0.85246" y2="0.10492"/> <atom id="ADP-atom26" elementType="C" x2="0.28197" y2="-0.17049"/> <atom id="ADP-atom27" elementType="O" x2="-0.36721" y2="-0.78689"/> <atom id="ADP-atom28" elementType="C" x2="0.53115" y2="-0.86557"/> <atom id="ADP-atom29" elementType="H" x2="0.77377" y2="-0.7377"/> <atom id="ADP-atom30" elementType="H" x2="0.92459" y2="-0.74426"/> <atom id="ADP-atom31" elementType="H" x2="0.60328" y2="-0.75082"/> <bond id="ADP-bond1" atomRefs="ADP-atom31 ADP-atom28" order="1"/> <bond id="ADP-bond2" atomRefs="ADP-atom30 ADP-atom8" order="1"/> <bond id="ADP-bond3" atomRefs="ADP-atom29 ADP-atom23" order="1"/> <bond id="ADP-bond4" atomRefs="ADP-atom28 ADP-atom23" order="1"/> <bond id="ADP-bond5" atomRefs="ADP-atom27 ADP-atom12" order="1"/> <bond id="ADP-bond6" atomRefs="ADP-atom26 ADP-atom3" order="A"/> <bond id="ADP-bond7" atomRefs="ADP-atom25 ADP-atom16" order="A"/> <bond id="ADP-bond8" atomRefs="ADP-atom24 ADP-atom6" order="1"/> <bond id="ADP-bond9" atomRefs="ADP-atom1 ADP-atom22" order="A"/> <bond id="ADP-bond10" atomRefs="ADP-atom22 ADP-atom25" order="A"/> <bond id="ADP-bond11" atomRefs="ADP-atom21 ADP-atom8" order="1"/> <bond id="ADP-bond12" atomRefs="ADP-atom22 ADP-atom20" order="A"/> <bond id="ADP-bond13" atomRefs="ADP-atom19 ADP-atom7" order="1"/> <bond id="ADP-bond14" atomRefs="ADP-atom18 ADP-atom12" order="1"/> <bond id="ADP-bond15" atomRefs="ADP-atom17 ADP-atom28" order="1"/> <bond id="ADP-bond16" atomRefs="ADP-atom16 ADP-atom14" order="A"/> <bond id="ADP-bond17" atomRefs="ADP-atom15 ADP-atom18" order="1"/> <bond id="ADP-bond18" atomRefs="ADP-atom13 ADP-atom20" order="1"/> <bond id="ADP-bond19" atomRefs="ADP-atom12 ADP-atom19" order="1"/> <bond id="ADP-bond20" atomRefs="ADP-atom11 ADP-atom23" order="1"/> <bond id="ADP-bond21" atomRefs="ADP-atom10 ADP-atom15" order="2"/> <bond id="ADP-bond22" atomRefs="ADP-atom9 ADP-atom15" order="1"/> <bond id="ADP-bond23" atomRefs="ADP-atom8 ADP-atom14" order="1"/> <bond id="ADP-bond24" atomRefs="ADP-atom8 ADP-atom23" order="1"/> <bond id="ADP-bond25" atomRefs="ADP-atom7 ADP-atom6" order="1"/> <bond id="ADP-bond26" atomRefs="ADP-atom6 ADP-atom21" order="1"/> <bond id="ADP-bond27" atomRefs="ADP-atom6 ADP-atom28" order="1"/> <bond id="ADP-bond28" atomRefs="ADP-atom5 ADP-atom12" order="2"/> <bond id="ADP-bond29" atomRefs="ADP-atom4 ADP-atom15" order="1"/> <bond id="ADP-bond30" atomRefs="ADP-atom3 ADP-atom1" order="A"/> <bond id="ADP-bond31" atomRefs="ADP-atom2 ADP-atom26" order="A"/> <bond id="ADP-bond32" atomRefs="ADP-atom20 ADP-atom2" order="A"/> <bond id="ADP-bond33" atomRefs="ADP-atom14 ADP-atom1" order="A"/> <formula concise="C 10 H 15 N 5 O 10 P 2" formalCharge="-3"/> 427.203 c12(n(cnc(c(N)ncn1)2)[CH]3(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)O))
<atom id="ARSENATE-atom1" elementType="AS" x2="0.0" y2="0.0"/> <atom id="ARSENATE-atom2" elementType="O" x2="0.9961977" y2="0.0" formalCharge="-1"/> <atom id="ARSENATE-atom3" elementType="O" x2="0.0" y2="0.9961977" formalCharge="-1"/> <atom id="ARSENATE-atom4" elementType="O" x2="0.0" y2="-1.0" formalCharge="-1"/> <atom id="ARSENATE-atom5" elementType="O" x2="-1.0" y2="0.0"/> <bond id="ARSENATE-bond1" atomRefs="ARSENATE-atom5 ARSENATE-atom1" order="2"/> <bond id="ARSENATE-bond2" atomRefs="ARSENATE-atom4 ARSENATE-atom1" order="1"/> <bond id="ARSENATE-bond3" atomRefs="ARSENATE-atom3 ARSENATE-atom1" order="1"/> <bond id="ARSENATE-bond4" atomRefs="ARSENATE-atom2 ARSENATE-atom1" order="1"/> <formula concise="O 4 AS 1" formalCharge="-3"/> 138.919 [As]([O-1])([O-1])(=O)[O-1]
<atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom1" elementType="O" x2="0.60784" y2="-1.0"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom2" elementType="O" x2="-1.0" y2="-0.53922"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom3" elementType="P" x2="0.60784" y2="-0.61111"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom4" elementType="O" x2="-0.38562" y2="-0.21242"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom5" elementType="C" x2="-0.38562" y2="-0.60131"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom6" elementType="O" x2="0.19608" y2="-0.61111"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom7" elementType="C" x2="-0.68954" y2="-0.77451"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom8" elementType="O" x2="0.99673" y2="-0.61111"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom9" elementType="O" x2="0.60784" y2="-0.22222"/> <atom id="DIHYDROXY-ACETONE-PHOSPHATE-atom10" elementType="C" x2="-0.07843" y2="-0.77451"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond1" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom10 DIHYDROXY-ACETONE-PHOSPHATE-atom6" order="1"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond2" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom9 DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="2"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond3" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom8 DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="1"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond4" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom7 DIHYDROXY-ACETONE-PHOSPHATE-atom5" order="1"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond5" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom6 DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="1"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond6" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom5 DIHYDROXY-ACETONE-PHOSPHATE-atom10" order="1"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond7" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom4 DIHYDROXY-ACETONE-PHOSPHATE-atom5" order="2"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond8" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom2 DIHYDROXY-ACETONE-PHOSPHATE-atom7" order="1"/> <bond id="DIHYDROXY-ACETONE-PHOSPHATE-bond9" atomRefs="DIHYDROXY-ACETONE-PHOSPHATE-atom1 DIHYDROXY-ACETONE-PHOSPHATE-atom3" order="1"/> <formula concise="C 3 H 7 O 6 P 1" formalCharge="0"/> 170.058 C(O)C(=O)COP(O)(=O)O
<atom id="GDP-atom1" elementType="N" x2="-0.05666667" y2="0.06666667"/> <atom id="GDP-atom2" elementType="H" x2="0.99666667" y2="-0.7366667"/> <atom id="GDP-atom3" elementType="N" x2="0.99666667" y2="0.2"/> <atom id="GDP-atom4" elementType="N" x2="0.4" y2="0.046666667"/> <atom id="GDP-atom5" elementType="N" x2="0.18" y2="0.44"/> <atom id="GDP-atom6" elementType="C" x2="0.26666668" y2="-0.39333335"/> <atom id="GDP-atom7" elementType="C" x2="0.99666667" y2="0.42333335"/> <atom id="GDP-atom8" elementType="O" x2="-0.7266667" y2="-0.12"/> <atom id="GDP-atom9" elementType="N" x2="0.81666666" y2="0.5466667"/> <atom id="GDP-atom10" elementType="O" x2="0.41333333" y2="-1.0"/> <atom id="GDP-atom11" elementType="C" x2="0.62" y2="0.44"/> <atom id="GDP-atom12" elementType="H" x2="0.41333333" y2="-0.67333335"/> <atom id="GDP-atom13" elementType="O" x2="-0.25333333" y2="-0.6666667"/> <atom id="GDP-atom14" elementType="O" x2="0.85333335" y2="-1.0"/> <atom id="GDP-atom15" elementType="O" x2="-0.25333333" y2="-0.12"/> <atom id="GDP-atom16" elementType="H" x2="0.0" y2="0.54333335"/> <atom id="GDP-atom17" elementType="O" x2="0.4" y2="0.85"/> <atom id="GDP-atom18" elementType="H" x2="0.85333335" y2="-0.67333335"/> <atom id="GDP-atom19" elementType="C" x2="0.26666668" y2="-0.5733333"/> <atom id="GDP-atom20" elementType="C" x2="0.4" y2="0.57666665"/> <atom id="GDP-atom21" elementType="O" x2="-0.7266667" y2="-0.6666667"/> <atom id="GDP-atom22" elementType="H" x2="0.26666668" y2="-0.7366667"/> <atom id="GDP-atom23" elementType="P" x2="-0.25333333" y2="-0.39333335"/> <atom id="GDP-atom24" elementType="C" x2="0.85333335" y2="-0.83666664"/> <atom id="GDP-atom25" elementType="O" x2="-1.0" y2="-0.39333335"/> <atom id="GDP-atom26" elementType="O" x2="-0.45" y2="-0.39333335"/> <atom id="GDP-atom27" elementType="C" x2="0.99666667" y2="-0.5733333"/> <atom id="GDP-atom28" elementType="C" x2="0.18" y2="0.2"/> <atom id="GDP-atom29" elementType="C" x2="0.41333333" y2="-0.83666664"/> <atom id="GDP-atom30" elementType="C" x2="0.62" y2="0.2"/> <atom id="GDP-atom31" elementType="O" x2="0.62666667" y2="-0.35666665"/> <atom id="GDP-atom32" elementType="P" x2="-0.7266667" y2="-0.39333335"/> <atom id="GDP-atom33" elementType="O" x2="0.02" y2="-0.39333335"/> <bond id="GDP-bond1" atomRefs="GDP-atom33 GDP-atom6" order="1"/> <bond id="GDP-bond2" atomRefs="GDP-atom32 GDP-atom26" order="1"/> <bond id="GDP-bond3" atomRefs="GDP-atom31 GDP-atom27" order="1"/> <bond id="GDP-bond4" atomRefs="GDP-atom30 GDP-atom4" order="A"/> <bond id="GDP-bond5" atomRefs="GDP-atom30 GDP-atom3" order="A"/> <bond id="GDP-bond6" atomRefs="GDP-atom29 GDP-atom24" order="1"/> <bond id="GDP-bond7" atomRefs="GDP-atom28 GDP-atom5" order="A"/> <bond id="GDP-bond8" atomRefs="GDP-atom27 GDP-atom24" order="1"/> <bond id="GDP-bond9" atomRefs="GDP-atom27 GDP-atom3" order="1"/> <bond id="GDP-bond10" atomRefs="GDP-atom26 GDP-atom23" order="1"/> <bond id="GDP-bond11" atomRefs="GDP-atom25 GDP-atom32" order="2"/> <bond id="GDP-bond12" atomRefs="GDP-atom23 GDP-atom33" order="1"/> <bond id="GDP-bond13" atomRefs="GDP-atom22 GDP-atom19" order="1"/> <bond id="GDP-bond14" atomRefs="GDP-atom21 GDP-atom32" order="1"/> <bond id="GDP-bond15" atomRefs="GDP-atom20 GDP-atom11" order="A"/> <bond id="GDP-bond16" atomRefs="GDP-atom19 GDP-atom29" order="1"/> <bond id="GDP-bond17" atomRefs="GDP-atom19 GDP-atom31" order="1"/> <bond id="GDP-bond18" atomRefs="GDP-atom18 GDP-atom24" order="1"/> <bond id="GDP-bond19" atomRefs="GDP-atom17 GDP-atom20" order="2"/> <bond id="GDP-bond20" atomRefs="GDP-atom16 GDP-atom5" order="1"/> <bond id="GDP-bond21" atomRefs="GDP-atom15 GDP-atom23" order="2"/> <bond id="GDP-bond22" atomRefs="GDP-atom14 GDP-atom24" order="1"/> <bond id="GDP-bond23" atomRefs="GDP-atom13 GDP-atom23" order="1"/> <bond id="GDP-bond24" atomRefs="GDP-atom12 GDP-atom29" order="1"/> <bond id="GDP-bond25" atomRefs="GDP-atom11 GDP-atom30" order="A"/> <bond id="GDP-bond26" atomRefs="GDP-atom10 GDP-atom29" order="1"/> <bond id="GDP-bond27" atomRefs="GDP-atom9 GDP-atom11" order="A"/> <bond id="GDP-bond28" atomRefs="GDP-atom8 GDP-atom32" order="1"/> <bond id="GDP-bond29" atomRefs="GDP-atom7 GDP-atom9" order="A"/> <bond id="GDP-bond30" atomRefs="GDP-atom6 GDP-atom19" order="1"/> <bond id="GDP-bond31" atomRefs="GDP-atom5 GDP-atom20" order="A"/> <bond id="GDP-bond32" atomRefs="GDP-atom4 GDP-atom28" order="A"/> <bond id="GDP-bond33" atomRefs="GDP-atom3 GDP-atom7" order="A"/> <bond id="GDP-bond34" atomRefs="GDP-atom2 GDP-atom27" order="1"/> <bond id="GDP-bond35" atomRefs="GDP-atom1 GDP-atom28" order="1"/> <formula concise="C 10 H 15 N 5 O 11 P 2" formalCharge="-3"/> 443.203 C(OP(O)(=O)OP(O)(=O)O)[CH]1(O[CH]([CH](O)[CH]1O)n2(c3(c(nc2)c(=O)[nH]c(n3)N)))
<atom id="FRUCTOSE-6P-atom1" elementType="O" x2="-0.41525424" y2="-0.3079096"/> <atom id="FRUCTOSE-6P-atom2" elementType="C" x2="-0.124293804" y2="-0.3079096"/> <atom id="FRUCTOSE-6P-atom3" elementType="H" x2="0.028248549" y2="-0.65254235"/> <atom id="FRUCTOSE-6P-atom4" elementType="C" x2="-0.124293804" y2="-0.519774"/> <atom id="FRUCTOSE-6P-atom5" elementType="H" x2="-0.124293804" y2="-0.6949153"/> <atom id="FRUCTOSE-6P-atom6" elementType="O" x2="0.6751412" y2="-0.279661"/> <atom id="FRUCTOSE-6P-atom7" elementType="O" x2="0.028248549" y2="-1.0"/> <atom id="FRUCTOSE-6P-atom8" elementType="O" x2="0.27966106" y2="-0.29378533"/> <atom id="FRUCTOSE-6P-atom9" elementType="O" x2="0.9971751" y2="-0.7485876"/> <atom id="FRUCTOSE-6P-atom10" elementType="P" x2="-0.70903957" y2="-0.3079096"/> <atom id="FRUCTOSE-6P-atom11" elementType="C" x2="0.67231643" y2="-0.519774"/> <atom id="FRUCTOSE-6P-atom12" elementType="H" x2="0.52259886" y2="-1.0"/> <atom id="FRUCTOSE-6P-atom13" elementType="O" x2="-0.70903957" y2="-0.60169494"/> <atom id="FRUCTOSE-6P-atom14" elementType="C" x2="0.52259886" y2="-0.8248588"/> <atom id="FRUCTOSE-6P-atom15" elementType="O" x2="-1.0" y2="-0.3079096"/> <atom id="FRUCTOSE-6P-atom16" elementType="O" x2="-0.70903957" y2="-0.005649686"/> <atom id="FRUCTOSE-6P-atom17" elementType="C" x2="0.67231643" y2="-0.7485876"/> <atom id="FRUCTOSE-6P-atom18" elementType="C" x2="0.028248549" y2="-0.8248588"/> <atom id="FRUCTOSE-6P-atom19" elementType="O" x2="0.52259886" y2="-0.65254235"/> <bond id="FRUCTOSE-6P-bond1" atomRefs="FRUCTOSE-6P-atom19 FRUCTOSE-6P-atom14" order="1"/> <bond id="FRUCTOSE-6P-bond2" atomRefs="FRUCTOSE-6P-atom18 FRUCTOSE-6P-atom14" order="1"/> <bond id="FRUCTOSE-6P-bond3" atomRefs="FRUCTOSE-6P-atom17 FRUCTOSE-6P-atom11" order="1"/> <bond id="FRUCTOSE-6P-bond4" atomRefs="FRUCTOSE-6P-atom15 FRUCTOSE-6P-atom10" order="1"/> <bond id="FRUCTOSE-6P-bond5" atomRefs="FRUCTOSE-6P-atom13 FRUCTOSE-6P-atom10" order="1"/> <bond id="FRUCTOSE-6P-bond6" atomRefs="FRUCTOSE-6P-atom12 FRUCTOSE-6P-atom14" order="1"/> <bond id="FRUCTOSE-6P-bond7" atomRefs="FRUCTOSE-6P-atom11 FRUCTOSE-6P-atom14" order="1"/> <bond id="FRUCTOSE-6P-bond8" atomRefs="FRUCTOSE-6P-atom10 FRUCTOSE-6P-atom16" order="2"/> <bond id="FRUCTOSE-6P-bond9" atomRefs="FRUCTOSE-6P-atom10 FRUCTOSE-6P-atom1" order="1"/> <bond id="FRUCTOSE-6P-bond10" atomRefs="FRUCTOSE-6P-atom9 FRUCTOSE-6P-atom17" order="1"/> <bond id="FRUCTOSE-6P-bond11" atomRefs="FRUCTOSE-6P-atom8 FRUCTOSE-6P-atom11" order="1"/> <bond id="FRUCTOSE-6P-bond12" atomRefs="FRUCTOSE-6P-atom7 FRUCTOSE-6P-atom18" order="1"/> <bond id="FRUCTOSE-6P-bond13" atomRefs="FRUCTOSE-6P-atom6 FRUCTOSE-6P-atom11" order="1"/> <bond id="FRUCTOSE-6P-bond14" atomRefs="FRUCTOSE-6P-atom5 FRUCTOSE-6P-atom4" order="1"/> <bond id="FRUCTOSE-6P-bond15" atomRefs="FRUCTOSE-6P-atom4 FRUCTOSE-6P-atom18" order="1"/> <bond id="FRUCTOSE-6P-bond16" atomRefs="FRUCTOSE-6P-atom4 FRUCTOSE-6P-atom8" order="1"/> <bond id="FRUCTOSE-6P-bond17" atomRefs="FRUCTOSE-6P-atom3 FRUCTOSE-6P-atom18" order="1"/> <bond id="FRUCTOSE-6P-bond18" atomRefs="FRUCTOSE-6P-atom2 FRUCTOSE-6P-atom4" order="1"/> <bond id="FRUCTOSE-6P-bond19" atomRefs="FRUCTOSE-6P-atom1 FRUCTOSE-6P-atom2" order="1"/> <formula concise="C 6 H 13 O 9 P 1" formalCharge="0"/> 260.137 C(OP(O)(O)=O)[CH]1([CH](O)[CH](O)C(O)(O1)CO)
<atom id="CIT-atom1" elementType="O" x2="-0.62098" y2="0.17428"/> <atom id="CIT-atom2" elementType="O" x2="0.6176" y2="0.20135"/> <atom id="CIT-atom3" elementType="O" x2="-1.0" y2="-0.20474"/> <atom id="CIT-atom4" elementType="C" x2="-0.022" y2="-0.45516"/> <atom id="CIT-atom5" elementType="C" x2="-0.62098" y2="-0.20474"/> <atom id="CIT-atom6" elementType="C" x2="-0.022" y2="-0.7665"/> <atom id="CIT-atom7" elementType="C" x2="-0.47885" y2="-0.45516"/> <atom id="CIT-atom8" elementType="O" x2="-0.022" y2="-0.07614"/> <atom id="CIT-atom9" elementType="O" x2="0.27919" y2="-1.0"/> <atom id="CIT-atom10" elementType="C" x2="0.36379" y2="-0.45516"/> <atom id="CIT-atom11" elementType="O" x2="0.99662" y2="-0.17766"/> <atom id="CIT-atom12" elementType="O" x2="-0.3198" y2="-1.0"/> <atom id="CIT-atom13" elementType="C" x2="0.6176" y2="-0.17766"/> <bond id="CIT-bond1" atomRefs="CIT-atom13 CIT-atom10" order="1"/> <bond id="CIT-bond2" atomRefs="CIT-atom12 CIT-atom6" order="1"/> <bond id="CIT-bond3" atomRefs="CIT-atom11 CIT-atom13" order="1"/> <bond id="CIT-bond4" atomRefs="CIT-atom10 CIT-atom4" order="1"/> <bond id="CIT-bond5" atomRefs="CIT-atom9 CIT-atom6" order="2"/> <bond id="CIT-bond6" atomRefs="CIT-atom8 CIT-atom4" order="1"/> <bond id="CIT-bond7" atomRefs="CIT-atom7 CIT-atom4" order="1"/> <bond id="CIT-bond8" atomRefs="CIT-atom6 CIT-atom4" order="1"/> <bond id="CIT-bond9" atomRefs="CIT-atom5 CIT-atom7" order="1"/> <bond id="CIT-bond10" atomRefs="CIT-atom3 CIT-atom5" order="1"/> <bond id="CIT-bond11" atomRefs="CIT-atom2 CIT-atom13" order="2"/> <bond id="CIT-bond12" atomRefs="CIT-atom1 CIT-atom5" order="2"/> <formula concise="C 6 H 8 O 7" formalCharge="0"/> 192.125 C(=O)(O)CC(C(O)=O)(O)CC(O)=O
<atom id="GLC-6-P-atom1" elementType="H" x2="-1.0" y2="-0.13312"/> <atom id="GLC-6-P-atom2" elementType="C" x2="-0.68182" y2="0.32792"/> <atom id="GLC-6-P-atom3" elementType="O" x2="-0.37338" y2="0.62013"/> <atom id="GLC-6-P-atom4" elementType="O" x2="0.00974" y2="0.24351"/> <atom id="GLC-6-P-atom5" elementType="C" x2="-0.06494" y2="-0.77273"/> <atom id="GLC-6-P-atom6" elementType="P" x2="0.00974" y2="0.62013"/> <atom id="GLC-6-P-atom7" elementType="C" x2="0.26299" y2="-0.36039"/> <atom id="GLC-6-P-atom8" elementType="C" x2="-0.68182" y2="-0.77273"/> <atom id="GLC-6-P-atom9" elementType="O" x2="0.00974" y2="0.99675"/> <atom id="GLC-6-P-atom10" elementType="O" x2="-0.68182" y2="-0.54545"/> <atom id="GLC-6-P-atom11" elementType="H" x2="0.26299" y2="-0.13312"/> <atom id="GLC-6-P-atom12" elementType="C" x2="-1.0" y2="-0.36039"/> <atom id="GLC-6-P-atom13" elementType="H" x2="-0.06494" y2="-0.54545"/> <atom id="GLC-6-P-atom14" elementType="O" x2="-0.06494" y2="0.06494"/> <atom id="GLC-6-P-atom15" elementType="O" x2="0.38636" y2="0.62013"/> <atom id="GLC-6-P-atom16" elementType="O" x2="-0.06494" y2="-1.0"/> <atom id="GLC-6-P-atom17" elementType="C" x2="-0.68182" y2="0.06494"/> <atom id="GLC-6-P-atom18" elementType="O" x2="0.26299" y2="-0.58766"/> <atom id="GLC-6-P-atom19" elementType="H" x2="-0.68182" y2="-1.0"/> <atom id="GLC-6-P-atom20" elementType="O" x2="-1.0" y2="-0.58766"/> <atom id="GLC-6-P-atom21" elementType="H" x2="-0.68182" y2="-0.16234"/> <bond id="GLC-6-P-bond1" atomRefs="GLC-6-P-atom21 GLC-6-P-atom17" order="1"/> <bond id="GLC-6-P-bond2" atomRefs="GLC-6-P-atom20 GLC-6-P-atom12" order="1"/> <bond id="GLC-6-P-bond3" atomRefs="GLC-6-P-atom19 GLC-6-P-atom8" order="1"/> <bond id="GLC-6-P-bond4" atomRefs="GLC-6-P-atom18 GLC-6-P-atom7" order="1"/> <bond id="GLC-6-P-bond5" atomRefs="GLC-6-P-atom17 GLC-6-P-atom12" order="1"/> <bond id="GLC-6-P-bond6" atomRefs="GLC-6-P-atom16 GLC-6-P-atom5" order="1"/> <bond id="GLC-6-P-bond7" atomRefs="GLC-6-P-atom15 GLC-6-P-atom6" order="1"/> <bond id="GLC-6-P-bond8" atomRefs="GLC-6-P-atom14 GLC-6-P-atom17" order="1"/> <bond id="GLC-6-P-bond9" atomRefs="GLC-6-P-atom14 GLC-6-P-atom7" order="1"/> <bond id="GLC-6-P-bond10" atomRefs="GLC-6-P-atom13 GLC-6-P-atom5" order="1"/> <bond id="GLC-6-P-bond11" atomRefs="GLC-6-P-atom12 GLC-6-P-atom8" order="1"/> <bond id="GLC-6-P-bond12" atomRefs="GLC-6-P-atom11 GLC-6-P-atom7" order="1"/> <bond id="GLC-6-P-bond13" atomRefs="GLC-6-P-atom10 GLC-6-P-atom8" order="1"/> <bond id="GLC-6-P-bond14" atomRefs="GLC-6-P-atom9 GLC-6-P-atom6" order="2"/> <bond id="GLC-6-P-bond15" atomRefs="GLC-6-P-atom8 GLC-6-P-atom5" order="1"/> <bond id="GLC-6-P-bond16" atomRefs="GLC-6-P-atom7 GLC-6-P-atom5" order="1"/> <bond id="GLC-6-P-bond17" atomRefs="GLC-6-P-atom6 GLC-6-P-atom3" order="1"/> <bond id="GLC-6-P-bond18" atomRefs="GLC-6-P-atom4 GLC-6-P-atom6" order="1"/> <bond id="GLC-6-P-bond19" atomRefs="GLC-6-P-atom3 GLC-6-P-atom2" order="1"/> <bond id="GLC-6-P-bond20" atomRefs="GLC-6-P-atom2 GLC-6-P-atom17" order="1"/> <bond id="GLC-6-P-bond21" atomRefs="GLC-6-P-atom1 GLC-6-P-atom12" order="1"/> <formula concise="C 6 H 13 O 9 P 1" formalCharge="0"/> 260.137 C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)
<atom id="GLYCEROL-3P-atom1" elementType="O" x2="-0.06931" y2="0.43564"/> <atom id="GLYCEROL-3P-atom2" elementType="O" x2="-1.0" y2="-0.29703"/> <atom id="GLYCEROL-3P-atom3" elementType="P" x2="0.63036" y2="-0.63036"/> <atom id="GLYCEROL-3P-atom4" elementType="O" x2="0.25413" y2="-0.88779"/> <atom id="GLYCEROL-3P-atom5" elementType="C" x2="-0.07261" y2="-0.26073"/> <atom id="GLYCEROL-3P-atom6" elementType="O" x2="0.36964" y2="-0.26073"/> <atom id="GLYCEROL-3P-atom7" elementType="C" x2="-0.72277" y2="0.06271"/> <atom id="GLYCEROL-3P-atom8" elementType="C" x2="-0.33003" y2="0.06271"/> <atom id="GLYCEROL-3P-atom9" elementType="O" x2="0.9967" y2="-0.35974"/> <atom id="GLYCEROL-3P-atom10" elementType="O" x2="0.90099" y2="-1.0"/> <bond id="GLYCEROL-3P-bond1" atomRefs="GLYCEROL-3P-atom10 GLYCEROL-3P-atom3" order="1"/> <bond id="GLYCEROL-3P-bond2" atomRefs="GLYCEROL-3P-atom9 GLYCEROL-3P-atom3" order="2"/> <bond id="GLYCEROL-3P-bond3" atomRefs="GLYCEROL-3P-atom8 GLYCEROL-3P-atom5" order="1"/> <bond id="GLYCEROL-3P-bond4" atomRefs="GLYCEROL-3P-atom7 GLYCEROL-3P-atom8" order="1"/> <bond id="GLYCEROL-3P-bond5" atomRefs="GLYCEROL-3P-atom6 GLYCEROL-3P-atom3" order="1"/> <bond id="GLYCEROL-3P-bond6" atomRefs="GLYCEROL-3P-atom5 GLYCEROL-3P-atom6" order="1"/> <bond id="GLYCEROL-3P-bond7" atomRefs="GLYCEROL-3P-atom4 GLYCEROL-3P-atom3" order="1"/> <bond id="GLYCEROL-3P-bond8" atomRefs="GLYCEROL-3P-atom2 GLYCEROL-3P-atom7" order="1"/> <bond id="GLYCEROL-3P-bond9" atomRefs="GLYCEROL-3P-atom1 GLYCEROL-3P-atom8" order="1"/> <formula concise="C 3 H 9 O 6 P 1" formalCharge="0"/> 172.074 C(C(O)CO)OP(=O)(O)O
<atom id="PROTON-atom1" elementType="H" x2="-1.0" y2="-1.0" formalCharge="1"/> <formula concise="H 1" formalCharge="1"/> 1.008 [H+1]
<atom id="FRUCTOSE-16-DIPHOSPHATE-atom1" elementType="H" x2="0.16364" y2="-0.97355"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom2" elementType="C" x2="0.28595" y2="-0.7686"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom3" elementType="C" x2="-0.34876" y2="-0.42149"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom4" elementType="H" x2="-0.34876" y2="-0.72893"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom5" elementType="O" x2="0.76529" y2="-0.53719"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom6" elementType="C" x2="0.28595" y2="-0.59008"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom7" elementType="P" x2="0.76529" y2="-0.7686"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom8" elementType="C" x2="-0.34876" y2="-0.59008"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom9" elementType="C" x2="0.16364" y2="-0.83471"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom10" elementType="O" x2="0.5405" y2="-0.7686"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom11" elementType="O" x2="0.28595" y2="-0.35868"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom12" elementType="O" x2="0.99669" y2="-0.7686"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom13" elementType="P" x2="-0.7686" y2="-0.42149"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom14" elementType="H" x2="-0.22645" y2="-0.69587"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom15" elementType="O" x2="-1.0" y2="-0.42149"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom16" elementType="O" x2="-0.0281" y2="-0.41157"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom17" elementType="O" x2="-0.7686" y2="-0.2"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom18" elementType="O" x2="-0.53388" y2="-0.42149"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom19" elementType="C" x2="-0.22645" y2="-0.83471"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom20" elementType="O" x2="0.76529" y2="-1.0"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom21" elementType="O" x2="-0.7686" y2="-0.66281"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom22" elementType="O" x2="0.16364" y2="-0.69587"/> <atom id="FRUCTOSE-16-DIPHOSPHATE-atom23" elementType="O" x2="-0.22645" y2="-0.97355"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond1" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom23 FRUCTOSE-16-DIPHOSPHATE-atom19" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond2" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom22 FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond3" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom21 FRUCTOSE-16-DIPHOSPHATE-atom13" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond4" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom20 FRUCTOSE-16-DIPHOSPHATE-atom7" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond5" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom19 FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond6" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom18 FRUCTOSE-16-DIPHOSPHATE-atom3" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond7" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom17 FRUCTOSE-16-DIPHOSPHATE-atom13" order="2"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond8" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom16 FRUCTOSE-16-DIPHOSPHATE-atom6" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond9" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom15 FRUCTOSE-16-DIPHOSPHATE-atom13" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond10" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom14 FRUCTOSE-16-DIPHOSPHATE-atom19" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond11" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom13 FRUCTOSE-16-DIPHOSPHATE-atom18" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond12" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom12 FRUCTOSE-16-DIPHOSPHATE-atom7" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond13" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom11 FRUCTOSE-16-DIPHOSPHATE-atom6" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond14" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom10 FRUCTOSE-16-DIPHOSPHATE-atom2" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond15" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom8 FRUCTOSE-16-DIPHOSPHATE-atom19" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond16" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom8 FRUCTOSE-16-DIPHOSPHATE-atom16" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond17" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom7 FRUCTOSE-16-DIPHOSPHATE-atom10" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond18" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom6 FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond19" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom5 FRUCTOSE-16-DIPHOSPHATE-atom7" order="2"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond20" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom4 FRUCTOSE-16-DIPHOSPHATE-atom8" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond21" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom3 FRUCTOSE-16-DIPHOSPHATE-atom8" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond22" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom2 FRUCTOSE-16-DIPHOSPHATE-atom6" order="1"/> <bond id="FRUCTOSE-16-DIPHOSPHATE-bond23" atomRefs="FRUCTOSE-16-DIPHOSPHATE-atom1 FRUCTOSE-16-DIPHOSPHATE-atom9" order="1"/> <formula concise="C 6 H 14 O 12 P 2" formalCharge="0"/> 340.117 C(OP(O)(O)=O)C1(O)(O[CH]([CH](O)[CH](O)1)COP(=O)(O)O) D-Fructose 1,6-bis(dihydrogenphosphate)
<atom id="ATP-atom1" elementType="C" x2="0.9971347" y2="-0.16905439"/> <atom id="ATP-atom2" elementType="P" x2="-0.4641834" y2="-0.68767905"/> <atom id="ATP-atom3" elementType="O" x2="-1.0" y2="-0.68767905"/> <atom id="ATP-atom4" elementType="N" x2="0.8767909" y2="-0.022922575"/> <atom id="ATP-atom5" elementType="O" x2="-0.12320912" y2="-0.5071633"/> <atom id="ATP-atom6" elementType="H" x2="0.5616046" y2="-0.8538682"/> <atom id="ATP-atom7" elementType="H" x2="0.6418339" y2="-0.7851003"/> <atom id="ATP-atom8" elementType="O" x2="-0.12320912" y2="-0.8653295"/> <atom id="ATP-atom9" elementType="O" x2="-0.4641834" y2="-0.8653295"/> <atom id="ATP-atom10" elementType="C" x2="0.5616046" y2="-0.7449857"/> <atom id="ATP-atom11" elementType="N" x2="0.8939829" y2="-0.3409742"/> <atom id="ATP-atom12" elementType="C" x2="0.6418339" y2="-0.89111745"/> <atom id="ATP-atom13" elementType="O" x2="-0.4641834" y2="-0.5071633"/> <atom id="ATP-atom14" elementType="C" x2="0.8939829" y2="-0.739255"/> <atom id="ATP-atom15" elementType="C" x2="0.82234967" y2="-0.89111745"/> <atom id="ATP-atom16" elementType="N" x2="0.4068768" y2="-0.10315186"/> <atom id="ATP-atom17" elementType="C" x2="0.4068768" y2="-0.29226357"/> <atom id="ATP-atom18" elementType="N" x2="0.5587393" y2="-0.3925501"/> <atom id="ATP-atom19" elementType="N" x2="0.5587393" y2="0.17478514"/> <atom id="ATP-atom20" elementType="O" x2="0.82234967" y2="-1.0"/> <atom id="ATP-atom21" elementType="C" x2="0.72206306" y2="-0.10315186"/> <atom id="ATP-atom22" elementType="C" x2="0.72206306" y2="-0.29226357"/> <atom id="ATP-atom23" elementType="C" x2="0.5587393" y2="-0.0028653145"/> <atom id="ATP-atom24" elementType="O" x2="0.6418339" y2="-1.0"/> <atom id="ATP-atom25" elementType="P" x2="-0.12320912" y2="-0.68767905"/> <atom id="ATP-atom26" elementType="H" x2="0.82234967" y2="-0.7851003"/> <atom id="ATP-atom27" elementType="O" x2="-0.81948423" y2="-0.8653295"/> <atom id="ATP-atom28" elementType="H" x2="0.8939829" y2="-0.8481375"/> <atom id="ATP-atom29" elementType="C" x2="0.36389685" y2="-0.68767905"/> <atom id="ATP-atom30" elementType="O" x2="0.7306591" y2="-0.66762173"/> <atom id="ATP-atom31" elementType="O" x2="-0.29226357" y2="-0.68767905"/> <atom id="ATP-atom32" elementType="O" x2="-0.81948423" y2="-0.5071633"/> <atom id="ATP-atom33" elementType="O" x2="0.05157602" y2="-0.68767905"/> <atom id="ATP-atom34" elementType="P" x2="-0.81948423" y2="-0.68767905"/> <atom id="ATP-atom35" elementType="O" x2="-0.63610315" y2="-0.68767905"/> <bond id="ATP-bond1" atomRefs="ATP-atom35 ATP-atom2" order="1"/> <bond id="ATP-bond2" atomRefs="ATP-atom34 ATP-atom35" order="1"/> <bond id="ATP-bond3" atomRefs="ATP-atom33 ATP-atom29" order="1"/> <bond id="ATP-bond4" atomRefs="ATP-atom32 ATP-atom34" order="2"/> <bond id="ATP-bond5" atomRefs="ATP-atom31 ATP-atom25" order="1"/> <bond id="ATP-bond6" atomRefs="ATP-atom30 ATP-atom14" order="1"/> <bond id="ATP-bond7" atomRefs="ATP-atom29 ATP-atom10" order="1"/> <bond id="ATP-bond8" atomRefs="ATP-atom28 ATP-atom14" order="1"/> <bond id="ATP-bond9" atomRefs="ATP-atom27 ATP-atom34" order="1"/> <bond id="ATP-bond10" atomRefs="ATP-atom26 ATP-atom15" order="1"/> <bond id="ATP-bond11" atomRefs="ATP-atom25 ATP-atom33" order="1"/> <bond id="ATP-bond12" atomRefs="ATP-atom24 ATP-atom12" order="1"/> <bond id="ATP-bond13" atomRefs="ATP-atom23 ATP-atom16" order="A"/> <bond id="ATP-bond14" atomRefs="ATP-atom22 ATP-atom21" order="A"/> <bond id="ATP-bond15" atomRefs="ATP-atom21 ATP-atom4" order="A"/> <bond id="ATP-bond16" atomRefs="ATP-atom21 ATP-atom23" order="A"/> <bond id="ATP-bond17" atomRefs="ATP-atom20 ATP-atom15" order="1"/> <bond id="ATP-bond18" atomRefs="ATP-atom19 ATP-atom23" order="1"/> <bond id="ATP-bond19" atomRefs="ATP-atom18 ATP-atom22" order="A"/> <bond id="ATP-bond20" atomRefs="ATP-atom17 ATP-atom18" order="A"/> <bond id="ATP-bond21" atomRefs="ATP-atom16 ATP-atom17" order="A"/> <bond id="ATP-bond22" atomRefs="ATP-atom14 ATP-atom15" order="1"/> <bond id="ATP-bond23" atomRefs="ATP-atom14 ATP-atom11" order="1"/> <bond id="ATP-bond24" atomRefs="ATP-atom13 ATP-atom2" order="2"/> <bond id="ATP-bond25" atomRefs="ATP-atom12 ATP-atom15" order="1"/> <bond id="ATP-bond26" atomRefs="ATP-atom11 ATP-atom22" order="A"/> <bond id="ATP-bond27" atomRefs="ATP-atom10 ATP-atom12" order="1"/> <bond id="ATP-bond28" atomRefs="ATP-atom10 ATP-atom30" order="1"/> <bond id="ATP-bond29" atomRefs="ATP-atom9 ATP-atom2" order="1"/> <bond id="ATP-bond30" atomRefs="ATP-atom8 ATP-atom25" order="1"/> <bond id="ATP-bond31" atomRefs="ATP-atom7 ATP-atom12" order="1"/> <bond id="ATP-bond32" atomRefs="ATP-atom6 ATP-atom10" order="1"/> <bond id="ATP-bond33" atomRefs="ATP-atom5 ATP-atom25" order="2"/> <bond id="ATP-bond34" atomRefs="ATP-atom4 ATP-atom1" order="A"/> <bond id="ATP-bond35" atomRefs="ATP-atom3 ATP-atom34" order="1"/> <bond id="ATP-bond36" atomRefs="ATP-atom2 ATP-atom31" order="1"/> <bond id="ATP-bond37" atomRefs="ATP-atom1 ATP-atom11" order="A"/> <formula concise="C 10 H 16 N 5 O 13 P 3" formalCharge="-4"/> 507.183 [CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)OP(O)(=O)O)
<atom id="DPG-atom1" elementType="C" x2="-0.02174" y2="-0.73602"/> <atom id="DPG-atom2" elementType="P" x2="0.73292" y2="-0.48137"/> <atom id="DPG-atom3" elementType="O" x2="0.73292" y2="-0.21739"/> <atom id="DPG-atom4" elementType="P" x2="-0.73602" y2="-0.48137"/> <atom id="DPG-atom5" elementType="O" x2="0.49379" y2="-0.48137"/> <atom id="DPG-atom6" elementType="O" x2="-0.73602" y2="-0.21739"/> <atom id="DPG-atom7" elementType="O" x2="-0.52484" y2="-0.48137"/> <atom id="DPG-atom8" elementType="O" x2="-0.02174" y2="-1.0"/> <atom id="DPG-atom9" elementType="C" x2="-0.25776" y2="-0.48137"/> <atom id="DPG-atom10" elementType="O" x2="0.99689" y2="-0.48137"/> <atom id="DPG-atom11" elementType="O" x2="-0.25776" y2="-0.21739"/> <atom id="DPG-atom12" elementType="O" x2="-0.73602" y2="-0.74534"/> <atom id="DPG-atom13" elementType="O" x2="0.73292" y2="-0.74534"/> <atom id="DPG-atom14" elementType="O" x2="-1.0" y2="-0.48137"/> <atom id="DPG-atom15" elementType="C" x2="0.21739" y2="-0.48137"/> <bond id="DPG-bond1" atomRefs="DPG-atom15 DPG-atom5" order="1"/> <bond id="DPG-bond2" atomRefs="DPG-atom9 DPG-atom1" order="1"/> <bond id="DPG-bond3" atomRefs="DPG-atom9 DPG-atom11" order="2"/> <bond id="DPG-bond4" atomRefs="DPG-atom7 DPG-atom9" order="1"/> <bond id="DPG-bond5" atomRefs="DPG-atom5 DPG-atom2" order="1"/> <bond id="DPG-bond6" atomRefs="DPG-atom4 DPG-atom7" order="1"/> <bond id="DPG-bond7" atomRefs="DPG-atom4 DPG-atom6" order="1"/> <bond id="DPG-bond8" atomRefs="DPG-atom4 DPG-atom12" order="1"/> <bond id="DPG-bond9" atomRefs="DPG-atom4 DPG-atom14" order="2"/> <bond id="DPG-bond10" atomRefs="DPG-atom2 DPG-atom3" order="1"/> <bond id="DPG-bond11" atomRefs="DPG-atom2 DPG-atom13" order="1"/> <bond id="DPG-bond12" atomRefs="DPG-atom2 DPG-atom10" order="2"/> <bond id="DPG-bond13" atomRefs="DPG-atom1 DPG-atom15" order="1"/> <bond id="DPG-bond14" atomRefs="DPG-atom1 DPG-atom8" order="1"/> <formula concise="C 3 H 8 O 10 P 2" formalCharge="0"/> 266.038 C(OP(O)(O)=O)(=O)C(O)COP(O)(O)=O
<atom id="G3P-atom1" elementType="C" x2="5.7" y2="-0.5"/> <atom id="G3P-atom2" elementType="C" x2="5.7" y2="-1.25"/> <atom id="G3P-atom3" elementType="C" x2="5.6995" y2="0.25"/> <atom id="G3P-atom4" elementType="O" x2="6.3499" y2="0.6232"/> <atom id="G3P-atom5" elementType="O" x2="5.0484" y2="0.6225"/> <atom id="G3P-atom6" elementType="O" x2="6.45" y2="-0.4998"/> <atom id="G3P-atom7" elementType="P" x2="7.0977" y2="-1.6376"/> <atom id="G3P-atom8" elementType="O" x2="7.0887" y2="-2.3709"/> <atom id="G3P-atom9" elementType="O" x2="7.8767" y2="-1.6513"/> <atom id="G3P-atom10" elementType="O" x2="7.1108" y2="-0.9002"/> <atom id="G3P-atom11" elementType="O" x2="6.3477" y2="-1.6285"/> <bond id="G3P-bond1" atomRefs="G3P-atom7 G3P-atom11" order="1"/> <bond id="G3P-bond2" atomRefs="G3P-atom7 G3P-atom10" order="1"/> <bond id="G3P-bond3" atomRefs="G3P-atom7 G3P-atom9" order="2"/> <bond id="G3P-bond4" atomRefs="G3P-atom7 G3P-atom8" order="1"/> <bond id="G3P-bond5" atomRefs="G3P-atom2 G3P-atom11" order="1"/> <bond id="G3P-bond6" atomRefs="G3P-atom1 G3P-atom6" order="1"/> <bond id="G3P-bond7" atomRefs="G3P-atom1 G3P-atom3" order="1"/> <bond id="G3P-bond8" atomRefs="G3P-atom3 G3P-atom5" order="2"/> <bond id="G3P-bond9" atomRefs="G3P-atom3 G3P-atom4" order="1"/> <bond id="G3P-bond10" atomRefs="G3P-atom1 G3P-atom2" order="1"/> <formula concise="C 3 H 7 O 7 P 1" formalCharge="0"/> 186.058 C(OP(=O)(O)O)C(O)C(=O)O
<atom id="2-PG-atom1" elementType="C" x2="2.8208" y2="-1.4"/> <atom id="2-PG-atom2" elementType="C" x2="2.8208" y2="-0.65"/> <atom id="2-PG-atom3" elementType="O" x2="2.1713" y2="-1.775"/> <atom id="2-PG-atom4" elementType="O" x2="3.4704" y2="-1.775"/> <atom id="2-PG-atom5" elementType="C" x2="2.8208" y2="0.1"/> <atom id="2-PG-atom6" elementType="O" x2="3.4704" y2="0.475"/> <atom id="2-PG-atom7" elementType="P" x2="1.2603" y2="-0.6662"/> <atom id="2-PG-atom8" elementType="O" x2="1.2502" y2="0.0671"/> <atom id="2-PG-atom9" elementType="O" x2="0.452" y2="-0.652"/> <atom id="2-PG-atom10" elementType="O" x2="1.2663" y2="-1.4037"/> <atom id="2-PG-atom11" elementType="O" x2="2.0727" y2="-0.6505"/> <bond id="2-PG-bond1" atomRefs="2-PG-atom7 2-PG-atom11" order="1"/> <bond id="2-PG-bond2" atomRefs="2-PG-atom7 2-PG-atom10" order="1"/> <bond id="2-PG-bond3" atomRefs="2-PG-atom7 2-PG-atom9" order="2"/> <bond id="2-PG-bond4" atomRefs="2-PG-atom7 2-PG-atom8" order="1"/> <bond id="2-PG-bond5" atomRefs="2-PG-atom5 2-PG-atom6" order="1"/> <bond id="2-PG-bond6" atomRefs="2-PG-atom2 2-PG-atom5" order="1"/> <bond id="2-PG-bond7" atomRefs="2-PG-atom2 2-PG-atom11" order="1"/> <bond id="2-PG-bond8" atomRefs="2-PG-atom1 2-PG-atom4" order="2"/> <bond id="2-PG-bond9" atomRefs="2-PG-atom1 2-PG-atom3" order="1"/> <bond id="2-PG-bond10" atomRefs="2-PG-atom1 2-PG-atom2" order="1"/> <formula concise="C 3 H 7 O 7 P 1" formalCharge="0"/> 186.058 C(O)(=O)C(CO)OP(=O)(O)O
<atom id="MG+2-atom1" elementType="MG" x2="-1.0" y2="-1.0" formalCharge="2"/> <formula concise="MG 1" formalCharge="2"/> 24.305 [Mg+2]
<atom id="PHOSPHO-ENOL-PYRUVATE-atom1" elementType="O" x2="-0.57576" y2="-0.15789"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom2" elementType="O" x2="0.24721" y2="0.33652"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom3" elementType="O" x2="-1.0" y2="-0.57576"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom4" elementType="C" x2="-0.57576" y2="0.26635"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom5" elementType="C" x2="-0.9075" y2="0.52791"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom6" elementType="O" x2="-0.15152" y2="-0.57576"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom7" elementType="O" x2="-0.57576" y2="-1.0"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom8" elementType="O" x2="-0.10686" y2="0.99681"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom9" elementType="P" x2="-0.57576" y2="-0.57576"/> <atom id="PHOSPHO-ENOL-PYRUVATE-atom10" elementType="C" x2="-0.10686" y2="0.57257"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond1" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom10 PHOSPHO-ENOL-PYRUVATE-atom4" order="1"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond2" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom8 PHOSPHO-ENOL-PYRUVATE-atom10" order="2"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond3" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom7 PHOSPHO-ENOL-PYRUVATE-atom9" order="2"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond4" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom6 PHOSPHO-ENOL-PYRUVATE-atom9" order="1"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond5" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom5 PHOSPHO-ENOL-PYRUVATE-atom4" order="2"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond6" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom4 PHOSPHO-ENOL-PYRUVATE-atom1" order="1"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond7" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom3 PHOSPHO-ENOL-PYRUVATE-atom9" order="1"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond8" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom2 PHOSPHO-ENOL-PYRUVATE-atom10" order="1"/> <bond id="PHOSPHO-ENOL-PYRUVATE-bond9" atomRefs="PHOSPHO-ENOL-PYRUVATE-atom1 PHOSPHO-ENOL-PYRUVATE-atom9" order="1"/> <formula concise="C 3 H 5 O 6 P 1" formalCharge="0"/> 168.043 C=C(C(=O)O)OP(O)(=O)O
<atom id="WATER-atom1" elementType="O" x2="0.08287" y2="-0.19337"/> <atom id="WATER-atom2" elementType="H" x2="-1.0" y2="-0.74586"/> <atom id="WATER-atom3" elementType="H" x2="0.99448" y2="-1.0"/> <bond id="WATER-bond1" atomRefs="WATER-atom3 WATER-atom1" order="1"/> <bond id="WATER-bond2" atomRefs="WATER-atom2 WATER-atom1" order="1"/> <formula concise="H 2 O 1" formalCharge="0"/> 18.015 [OH2]
Pyruvate kinase I and pyruvate kinase II differ in physical and chemical properties as well as in their kinetic behavior. Although the two forms are under independent genetic control they do coexist in a wide range of nutritional and metabolic states. The two forms are not interconvertible. Both show positive cooperative effects with respect to the substrate phosphoenolpyruvate.|CITS:[83114522]| The enzyme has a low nucleotide specificity and the 5'-diphosphates of guanosine, inosine, uridine and cytidine can all serve as phospho acceptors.|CITS: [90336973]| Form I from E coli unlike form II is remarkably stable. |CITS:[91315755]|
E.coli is unusual in having two glyceraldehyde-3-phosphate dehydrogenases. The protein GAPDH-A has a sequence that is more similar to eukaryotic sequences than it is to prokaryotic types |CITS:[91087241]|. GapA is required for glycolysis, while Epd (GapB) is not |CITS: [9260967]|. GapA and Epd may be involved in production of pyridoxal 5'-phosphate (PLP) |CITS: [9696782]|.
This enzyme is an isozyme with phosphofructokinase-1. The nucleotide sequences of the genes are not similar.|CITS: [85203917]|
In relation to the Class I enzymes (primarily studied and found in eukaryotes) comparatively little is known about the class II enzymes. The Class II aldolases of Sacc. cer. and E. coli are the best characterized.|CITS: [89193446]| It resembles the typical class II aldolase from yeast in size and amino acid composition. This is a strong suggestion that they are related. |CITS:[78165651]| These less well studied aldolases are found both in the eukaryotic green algae and fungi, and in the prokaryotic blue-green algae and bacteria. |CITS:[78165651]| The gene pgk, encoding the enzyme phosphoglycerate kinase, was carried on plasmid pLC33-5 of the collection of Clarke and Carbon. It was also noted that E.coli cells tansformed with this plasmid exhibited raised levels of Class II fructose 1,6 bisphosphate aldolase activity, suggesting that the same plasmid might also carry the structural gene (fba) for this enzyme. |CITS: [89193446]|
The typical class I aldolases of plants and animals have been throroughly studied |CITS: [78165651]| Fructose-1,6-bisphosphate aldolases can be divided into two classes on the basis of their catalytic and structural properties. |CITS: [78165651]| Class I fructose 1,6 bisphosphate aldolases were once thought to be confined to eukaryotic organisms but have since been detected in several bacterial species. |CITS: [78165652]| The occurence of such an aldolase in bacteria was unexpected in light of the phylogenetic distribution of aldolases. |CITS: [73229139]| The enzymes of eukaryotes generally fall into Class I and are tetramers of identical polypeptide chains. |CITS: [89193446]| In earlier studies |CITS: [73229139]| it was thought that the class I E. coli aldolase was typical in that it was tetrameric with a mol. wt. of approx. 140K. In 1978 new purification techniques were used.The true aldolase 1 activity could be measured by using Fru-1,6-P2 that had been purified by chromatography on DEAE-cellulose to remove the fructose-6-phosphate. Using these methods the enzyme appeared to be larger than was previously supposed and may be a decamer with a mol. wt. of approx. 340,000. The size of aldolase 1 and the effect of cross-linking reagents on it, indicate that its structure must differ significantly from that of the typical tetrameric class-I enzymes from eukaryotes. |CITS: [78165652] [73229139]|
This enzyme is an isozyme with phosphofructokinase-2. The nucleotide sequences of the genes are not similar |CITS: [85203917]|. The tetrameric species is the only one which can bind both substrates and effectors, and thus have both catalytic and regulatory properties. The C terminal end of the peptide is required for allosteric properties.|CITS: [90276415]| Crystal structures have been solved with and without activators and inhibitors. |CITS: [89342465], [89125622]|
The enzyme denatures in the absence of Mg. When E. coli enolase was treated with EDTA in attempts to remove all residual activity prior to the Mg activation studies, it was found that the enzyme was unstable in the absence of Mg and that substantial and irreversible loss of activity was observed after very short exposure of the enzyme to EDTA. |CITS:[72060411]|
high concentrations of Mg+2 and ADP |CITS:[89228557]|
An activator only at low Mg+2 and Ca+2 concentrations, otherwise it is an inhibitor. |CITS: [83282602]|
Vanadate strongly inhibits the enzyme. |CITS: [99364512]|
Pyruvate from glycolysis proceeds to the pyruvate dehydrogenase multienzyme complex, and the acetyl CoA produced then proceeds on to the superpathway of glyoxylate bypass and TCA.
This pathway is freely available to all users and may be redistributed in whole or in part provided proper source attribution is made. See http://biocyc.org/open-reg.shtml for more information.
Type I pyruvate kinase is made up of 522 amino acids. Neither type I nor II contains tryptophan. The two forms of the enzyme, I and II are different proteins.|CITS:[83114522]| Pyruvate kinase F was previously referred to as pyruvate kinase B, now as I |CITS:[84029179]| A free N-terminal amino acid can be detected in both forms of pyruvate kinase it corresponds to methionine for type I and serine for type II.|CITS:[83114522]| Comparison with the known primary structures shows that bacterial enzymes lack a substantial portion of the N-terminal sequence with respect to pyruvate kinases from vertebrates. |CITS:[91315755]|
There are 2 genes, pykA and pykF, for 2 isozymes
The enzyme has not been characterized and the subunit structure is unknown. However, phosphoglycerate mutase 1 is a homodimer.
A higher degree of sequence homology exists between E.coli and eucaryotic enzymes than betwen E. coli and the thermophilic bacterial enzyme |CITS:[85257641]|. Mutant exhibits a growth defect and also exhibits increased aggregation and lysis that are rescued by high-salt media |CITS: [9260967]|. Regulation has been described |CITS: [12672900]|. The regulation of the fkpA, gapA, and hslT genes is affected by evolution under conditions of chronic heat stress |CITS: [12672900]|.
glyceraldehyde 3-phosphate dehydrogenase-A monomer
Phosphoglycerate kinase is one of the proteins induced by anaerobiosis. |CITS:[89306676]| The gene is transcribed from two promoters, one immediately in front of an upstream gene coding for a 38-kDa polypeptide of unknown function. The pgk gene was also found to show growth phase regulation. A structural determinant for glycerate 3-P kinase is located near serA. The map order is speB-pgk-serA-lysA-argA-eno-cysC.|CITS:[76195925]| Pgk has similarity to an Edwardsiella ictaluri protein |CITS: [12542086]|.
The amino acid sequence of the E.coli Class II fructose-1,6-bisphosphate aldolase inferred from the DNA sequence of the fda gene is the first primary structure of a Class II aldolase to be established. There is no immediately apparent sequence homology with any of the Class I fructose-1,6-bisphosphate aldolases which have been widely studied. |CITS:[89193446]| An fda mutant exhibits a heat-sensitive defect in rRNA transcription that is elicited via altered abundance of ppGpp and of initiating NTPs |CITS: [14526031]|. Fda has similarity to an Edwardsiella ictaluri protein that provokes an immune response in catfish |CITS: [12542086]|.
phosphoglucose isomerase is found primarily in the cytoplasm
Regulation has been described |CITS: [11101675]|. Transcription is regulated by Fur |CITS: [11101675]|.
Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products.
Role of the C-terminal region in the allosteric properties of Escherichia coli phosphofructokinase-1.
Steady-state fluorescence of Escherichia coli phosphofructokinase reveals a regulatory role for ATP.
WH Freeman and Co., 3rd edition, New York, 1988
Adv Enzymol Relat Areas Mol Biol 1979;48;193-244
Characterization of Escherichia coli strains with gapA and gapB genes deleted.
Nucleotide sequence of the Escherichia coli gap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of D-glyceraldehyde-3-phosphate dehydrogenase.
Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12.
A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote.
The Enzymes, Vol.XIII Academic Press, New York 1976;3rd Edition
Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis.
Nucleotide sequence of gene pfkB encoding the minor phosphofructokinase of Escherichia coli K-12.
Regulatory properties of phosphofructokinase 2 from Escherichia coli.
Nucleotide sequence and high-level expression of the major Escherichia coli phosphofructokinase.
Phosphofructokinases from Escherichia coli. Purification and characterization of the nonallosteric isozyme.
Purification and characterization of two fructose diphosphate aldolases from Escherichia coli (Crookes' strain).
Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli.
Purification and characterization of the class-II D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes' strain).
Isolation and characterization of the phosphoglucose isomerase gene from Escherichia coli.
The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase.
Urea-induced inactivation, dissociation, and unfolding of the allosteric phosphofructokinase from Escherichia coli.
Intracellular pH effect upon phosphoglucose isomerase in Escherichia coli
pH dependence of the kinetic properties of allosteric phosphofructokinase from Escherichia coli.
Crystal structure of unliganded phosphofructokinase from Escherichia coli.
A conformational transition involved in antagonistic substrate binding to the allosteric phosphofructokinase from Escherichia coli.
The purification and characterization of Escherichia coli enolase.
dihydronicotinamide adenine dinucleotide
nicotinamide adenine dinucleotide reduced
nicotinamide adenine dinucleotide oxidized
2-hydroxy-1,2,3-propanetricarboxylic acid