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Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine
Biology and Chemistry Report
3EUB
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE
    Text enzyme catalysis, desulfo, substrate orientation, xanthine, FAD, Flavoprotein, Iron, Iron-sulfur, Metal-binding, Molybdenum, NAD, Oxidoreductase, Peroxisome

    Polymeric Molecules

    Chain 2,A,J,S
    Description Xanthine dehydrogenase/oxidase 
    Fragment 2Fe-2S ferredoxin-type domain, residues 1-165 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18134.2 
    Source Method natural source  
    Entity Name XD, XO, Xanthine oxidoreductase 
    Chain 3,B,K,T
    Description Xanthine dehydrogenase/oxidase 
    Fragment AD-binding PCMH-type domain, residues 224-528 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34024.9 
    Source Method natural source  
    Entity Name XD, XO, Xanthine oxidoreductase 
    Chain 4,C,L,U
    Description Xanthine dehydrogenase/oxidase 
    Fragment residues 571-1332 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 83835.9 
    Source Method natural source  
    Entity Name XD, XO, Xanthine oxidoreductase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    FAD  FLAVIN-ADENINE DINUCLEOTIDE  C27 H33 N9 O15 P2   785.55  View 
    FES  FE2/S2 (INORGANIC) CLUSTER  Fe2 S2   175.82  View 
    MOM  HYDROXY(DIOXO)MOLYBDENUM  H Mo O3   144.95  View 
    MTE  PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER  C10 H14 N5 O6 P S2   395.35  View 
    XAN  XANTHINE  C5 H4 N4 O2   152.11  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    2,A,J,S XDH_BOVIN P80457     
    3,B,K,T XDH_BOVIN P80457     
    4,C,L,U XDH_BOVIN P80457     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    2 a J S  1.17.1.4        
    2 a J S  1.17.3.2        
    3 B K T  1.17.1.4        
    3 B K T  1.17.3.2        
    4 C L U  1.17.1.4        
    4 C L U  1.17.3.2        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain 2,A,J,S
    GO ID   Ontology GO Term Definition
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    9055   Electron Carrier Activity  Any Molecular Entity That Serves As an Electron Acceptor and Electron Donor in an Electron Transport Chain. an Electron Transport Chain Is a Process in Which a Series of Electron Carriers Operate Together to Transfer Electrons From Donors to Any of Several Different Terminal Electron Acceptors to Generate a Transmembrane Electrochemical Gradient. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    51536   Iron Sulfur Cluster Binding  Interacting Selectively and Non Covalently with an Iron Sulfur Cluster a Combination of Iron and Sulfur Atoms. 
    51537   2 Iron 2 Sulfur Cluster Binding  Interacting Selectively and Non Covalently with a 2 Iron 2 Sulfur (2fe 2s) Cluster; This Cluster Consists of Two Iron Atoms with Two Inorganic Sulfur Atoms Found Between the Irons and Acting As Bridging Ligands. 
    Chain 3,B,K,T
    GO ID   Ontology GO Term Definition
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    8762   Udp N Acetylmuramate Dehydrogenase Activity  Catalysis of the Reaction: Udp N Acetylmuramate + Nadp+ = Udp N Acetyl 3 O (1 Carboxyvinyl) D Glucosamine + Nadph + H+. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    16614   Oxidoreductase Activity Acting On Ch Oh Group of Donors  Catalysis of an Oxidation Reduction (redox) Reaction in Which a Ch Oh Group Act As a Hydrogen or Electron Donor and Reduces a Hydrogen or Electron Acceptor. 
    50660   Flavin Adenine Dinucleotide Binding  Interacting Selectively and Non Covalently with FAD Flavin Adenine Dinucleotide the Coenzyme or the Prosthetic Group of Various Flavoprotein Oxidoreductase Enzymes in Either the Oxidized Form FAD or the Reduced Form Fadh2. 
    Chain 4,C,L,U
    GO ID   Ontology GO Term Definition
    55114   Oxidation Reduction Process  A Metabolic Process That Results in the Removal or Addition of One or More Electrons to or From a Substance with or Without the Concomitant Removal or Addition of a Proton or Protons. 
    16491   Oxidoreductase Activity  Catalysis of an Oxidation Reduction (redox) Reaction a Reversible Chemical Reaction in Which the Oxidation State of an Atom or Atoms Within a Molecule Is Altered. One Substrate Acts As a Hydrogen or Electron Donor and Becomes Oxidized While the Other Acts As Hydrogen or Electron Acceptor and Becomes Reduced. 
    43546   Molybdopterin Cofactor Binding  Interacting Selectively and Non Covalently with the Molybdopterin Cofactor (moco) Essential For the Catalytic Activity of Some Enzymes E.g. Sulfite Oxidase Xanthine Dehydrogenase and Aldehyde Oxidase. the Cofactor Consists of a Mononuclear Molybdenum (mo Molybdopterin) or Tungsten Ion (w Molybdopterin) Coordinated by One or Two Molybdopterin Ligands. 


     
  •   Gene Details   Hide

    Natural Source

    Chain 4,C,L,U
    Common Name Bovine
    Scientific Name Bos taurus  
    Secretion Bovine Milk
    Chain 3,B,K,T
    Common Name Bovine
    Scientific Name Bos taurus  
    Secretion Bovine Milk
    Chain 2,A,J,S
    Common Name Bovine
    Scientific Name Bos taurus  
    Secretion Bovine Milk

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 - 280960     xanthine dehydrogenase XDH