2D0T Oxidoreductase date Aug 08, 2005
title Crystal Structure Of 4-Phenylimidazole Bound Form Of Human Indoleamine 2,3-Dioxygenase
authors H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, Y.Shiro, Riken Structural 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: Pet-15b
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.070 98.027 130.951 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand HEM, NHE, PIM BindingDB enzyme Oxidoreductase E.C.1.13.11.42 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (2d0t.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (2d0t.pdb2.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 2D0T
  • CSU: Contacts of Structural Units for 2D0T
  • Likely Quarternary Molecular Structure file(s) for 2D0T
  • Structure Factors (383 Kb)
  • Retrieve 2D0T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D0T from S2C, [Save to disk]
  • Re-refined 2d0t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D0T 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 2D0T
  • 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 2D0T, from MSDmotif at EBI
  • Fold representative 2d0t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d0t_A] [2d0t] [2d0t_B]
  • SWISS-PROT database: [P14902]
  • Domain organization of [I23O1_HUMAN] by SWISSPFAM
  • Other resources with information on 2D0T
  • Community annotation for 2D0T 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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