2D0U Oxidoreductase date Aug 08, 2005
title Crystal Structure Of Cyanide Bound Form Of Human Indoleamine Dioxygenase
authors H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, Y.Shiro, Riken Str Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Indoleamine 2,3-Dioxygenase
Chain: A, B
Synonym: Ido, Indoleamine-Pyrrole 2,3-Dioxygenase
Ec: 1.13.11.42
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.213 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.352 97.089 129.378 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand CYN, HEM, NHE enzyme Oxidoreductase E.C.1.13.11.42 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • electron transfer activity


  • Primary referenceCrystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase., Sugimoto H, Oda S, Otsuki T, Hino T, Yoshida T, Shiro Y, Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2611-6. Epub 2006 Feb 13. PMID:16477023
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (2d0u.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (2d0u.pdb2.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 2D0U
  • CSU: Contacts of Structural Units for 2D0U
  • Likely Quarternary Molecular Structure file(s) for 2D0U
  • Structure Factors (126 Kb)
  • Retrieve 2D0U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D0U from S2C, [Save to disk]
  • Re-refined 2d0u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D0U 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 2D0U
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2D0U, from MSDmotif at EBI
  • Fold representative 2d0u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d0u] [2d0u_A] [2d0u_B]
  • SWISS-PROT database: [P14902]
  • Domain organization of [I23O1_HUMAN] by SWISSPFAM
  • Other resources with information on 2D0U
  • Community annotation for 2D0U at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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