2D0U	Oxidoreductase	date	Aug 08, 2005
title	Crystal Structure Of Cyanide 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: 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 Diffraction	resolution	3.40 Å
ligand	CYN, HEM, NHE	enzyme	Oxidoreductase E.C.1.13.11.42 BRENDA
Gene Ontology	Chain Function Process Component A, B tryptophan 2,3-dioxygenase a... electron carrier activity oxidoreductase activity oxidoreductase activity, act... indoleamine 2,3-dioxygenase ... metal ion binding cytokine production involved... positive regulation of T cel... positive regulation of chron... positive regulation of type ... tryptophan catabolic process... inflammatory response female pregnancy behavior tryptophan catabolic process... response to lipopolysacchari... negative regulation of inter... positive regulation of inter... multicellular organismal res... kynurenic acid biosynthetic ... cellular nitrogen compound m... negative regulation of T cel... positive regulation of apopt... small molecule metabolic pro... negative regulation of activ... oxidation-reduction process negative regulation of T cel... cytoplasm cytosol smooth muscle contractile fi... stereocilium bundle
Primary reference	Crystal 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 (132 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2D0U

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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_A] [2d0u_B] SWISS-PROT database: [P14902] Domain organization of [I23O1_HUMAN] by SWISSPFAM Alignments of the sequence of 2D0U with the sequences similar proteins can be viewed for 2D0U's classification [I23O1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [I23O1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2D0U

Community annotation for 2D0U at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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