1VDV Oxidoreductase date Mar 25, 2004
title Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
authors A.Fukunari, K.Okamoto, T.Nishino, B.T.Eger, E.F.Pai, M.Kamezawa, I N.Kato
compound source
Molecule: Xanthine Dehydrogenaseoxidase
Chain: A, B
Synonym: Xanthine Oxidoreductase
Ec: 1.1.1.204
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Secretion: Milk
symmetry Space Group: C 1 2 1
R_factor 0.178 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
166.817 123.940 148.888 90.00 91.16 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand ACY, CA, FAD, FES, GOL, MOS, MTE, YSH BindingDB enzyme Oxidoreductase E.C.1.1.1.204 BRENDA
related structures by homologous chain: 1FO4, 1V97
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • electron transfer activity


  • Primary referenceY-700 [1-[3-Cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid]: a potent xanthine oxidoreductase inhibitor with hepatic excretion., Fukunari A, Okamoto K, Nishino T, Eger BT, Pai EF, Kamezawa M, Yamada I, Kato N, J Pharmacol Exp Ther 2004 Nov;311(2):519-28. Epub 2004 Jun 09. PMID:15190124
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (455 Kb) [Save to disk]
  • Biological Unit Coordinates (1vdv.pdb1.gz) 447 Kb
  • LPC: Ligand-Protein Contacts for 1VDV
  • CSU: Contacts of Structural Units for 1VDV
  • Likely Quarternary Molecular Structure file(s) for 1VDV
  • Retrieve 1VDV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VDV from S2C, [Save to disk]
  • View 1VDV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1VDV
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VDV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vdva6, region A:192-414 [Jmol] [rasmolscript] [script source]
        - Domain d1vdva2, region A:3-92 [Jmol] [rasmolscript] [script source]
        - Domain d1vdva4, region A:415-528 [Jmol] [rasmolscript] [script source]
        - Domain d1vdva3, region A:537-694 [Jmol] [rasmolscript] [script source]
        - Domain d1vdva5, region A:695-1332 [Jmol] [rasmolscript] [script source]
        - Domain d1vdva1, region A:93-165 [Jmol] [rasmolscript] [script source]
        - Domain d1vdvb6, region B:192-414 [Jmol] [rasmolscript] [script source]
        - Domain d1vdvb2, region B:3-92 [Jmol] [rasmolscript] [script source]
        - Domain d1vdvb4, region B:415-528 [Jmol] [rasmolscript] [script source]
        - Domain d1vdvb3, region B:537-694 [Jmol] [rasmolscript] [script source]
        - Domain d1vdvb5, region B:695-1332 [Jmol] [rasmolscript] [script source]
        - Domain d1vdvb1, region B:93-165 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vdv_B] [1vdv] [1vdv_A]
  • SWISS-PROT database: [P80457]
  • Domain organization of [XDH_BOVIN] by SWISSPFAM
  • Domains found in 1VDV: [Ald_Xan_dh_C] [CO_deh_flav_C ] by SMART
  • Other resources with information on 1VDV
  • Community annotation for 1VDV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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