6UBP | pdb_00006ubp

Crystal structure of a photochemical intermediate of human indoleamine 2,3-dioxygenase 1 in complex with carbon monoxide and tryptophan

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6ubpb_	All alpha proteins	Indolic compounds 2,3-dioxygenase-like	Indolic compounds 2,3-dioxygenase-like	Indoleamine 2,3-dioxygenase-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6ubpa_	All alpha proteins	Indolic compounds 2,3-dioxygenase-like	Indolic compounds 2,3-dioxygenase-like	Indoleamine 2,3-dioxygenase-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	indolic compounds 2, 3-dioxygenase-like	8039469	3001961	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	indolic compounds 2, 3-dioxygenase-like	8039469	3001961	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	DUF1864_C	e6ubpB1	A: alpha bundles	X: Indolic compounds 2,3-dioxygenase-like (From Topology)	H: Indolic compounds 2,3-dioxygenase-like (From Topology)	T: Indolic compounds 2,3-dioxygenase-like	F: DUF1864_C	ECOD (1.6)
B	IDO	e6ubpB2	A: alpha superhelices	X: Indoleamine 2,3-dioxygenase N-terminal subdomain (From Topology)	H: Indoleamine 2,3-dioxygenase N-terminal subdomain (From Topology)	T: Indoleamine 2,3-dioxygenase N-terminal subdomain	F: IDO	ECOD (1.6)
A	DUF1864_C	e6ubpA1	A: alpha bundles	X: Indolic compounds 2,3-dioxygenase-like (From Topology)	H: Indolic compounds 2,3-dioxygenase-like (From Topology)	T: Indolic compounds 2,3-dioxygenase-like	F: DUF1864_C	ECOD (1.6)
A	IDO	e6ubpA2	A: alpha superhelices	X: Indoleamine 2,3-dioxygenase N-terminal subdomain (From Topology)	H: Indoleamine 2,3-dioxygenase N-terminal subdomain (From Topology)	T: Indoleamine 2,3-dioxygenase N-terminal subdomain	F: IDO	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01231	Indoleamine 2,3-dioxygenase (IDO)	Indoleamine 2,3-dioxygenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Indoleamine 2,3-dioxygenase 1	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity indoleamine 2,3-dioxygenase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity dioxygenase activity L-tryptophan 2,3-dioxygenase activity electron transfer activity binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity indoleamine 2,3-dioxygenase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity dioxygenase activity L-tryptophan 2,3-dioxygenase activity electron transfer activity binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	multi-multicellular organism process multicellular organismal process reproductive process female pregnancy multi-organism reproductive process oxoacid metabolic process NAD+ biosynthetic process nucleotide biosynthetic process indole-containing compound metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process multi-multicellular organism process multicellular organismal process reproductive process female pregnancy multi-organism reproductive process oxoacid metabolic process NAD+ biosynthetic process nucleotide biosynthetic process indole-containing compound metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process L-tryptophan metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process aromatic amino acid metabolic process pyridine-containing compound biosynthetic process carboxylic acid metabolic process 'de novo' NAD+ biosynthetic process from L-tryptophan primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process L-amino acid metabolic process purine-containing compound metabolic process nicotinamide nucleotide biosynthetic process proteinogenic amino acid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine nucleotide biosynthetic process behavior locomotory behavior swimming behavior negative regulation of lymphocyte proliferation regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation regulation of biological process cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion biological regulation cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation response to stimulus immune response positive regulation of biological process positive regulation of response to stimulus positive regulation of type 2 immune response type 2 immune response regulation of response to stimulus positive regulation of immune response regulation of type 2 immune response regulation of immune response positive regulation of immune system process monocarboxylic acid biosynthetic process small molecule biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process kynurenic acid biosynthetic process kynurenic acid metabolic process monocarboxylic acid metabolic process regulation of interleukin-12 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process interleukin-12 production positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of interleukin-12 production regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process response to stress multicellular organismal response to stress negative regulation of interleukin-10 production interleukin-10 production regulation of interleukin-10 production negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cytokine production negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process immune system development developmental process T cell tolerance induction positive regulation of T cell tolerance induction multicellular organism development anatomical structure development regulation of tolerance induction positive regulation of tolerance induction regulation of T cell tolerance induction tolerance induction system development catabolic process ketone metabolic process aromatic amino acid family catabolic process organic acid catabolic process non-proteinogenic amino acid metabolic process carboxylic acid catabolic process amino acid catabolic process L-tryptophan catabolic process to kynurenine benzene-containing compound metabolic process L-amino acid catabolic process L-tryptophan catabolic process kynurenine metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process indole-containing compound catabolic process small molecule catabolic process quinolinate metabolic process dicarboxylic acid metabolic process quinolinate biosynthetic process dicarboxylic acid biosynthetic process positive regulation of chronic inflammatory response regulation of defense response regulation of chronic inflammatory response chronic inflammatory response regulation of response to external stimulus defense response regulation of inflammatory response response to external stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress positive regulation of defense response inflammatory response regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process negative regulation of programmed cell death leukocyte apoptotic process regulation of apoptotic process regulation of programmed cell death cell death negative regulation of T cell apoptotic process lymphocyte apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process regulation of T cell apoptotic process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process positive regulation of apoptotic process positive regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process biological process involved in interspecies interaction between organisms response to lipid response to other organism response to oxygen-containing compound response to lipopolysaccharide response to biotic stimulus response to bacterium response to chemical response to external biotic stimulus response to molecule of bacterial origin	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol stereocilium bundle cluster of actin-based cell projections smooth muscle contractile fiber intracellular membraneless organelle intracellular organelle organelle membraneless organelle contractile muscle fiber supramolecular fiber supramolecular polymer cellular anatomical structure intracellular anatomical structure cytoplasm cytosol stereocilium bundle cluster of actin-based cell projections smooth muscle contractile fiber intracellular membraneless organelle intracellular organelle organelle membraneless organelle contractile muscle fiber supramolecular fiber supramolecular polymer supramolecular complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR037217	Tryptophan/Indoleamine 2,3-dioxygenase-like	Homologous Superfamily
A, B	IPR000898	Indoleamine 2,3-dioxygenase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P14902	endometriosis Neoplasm Recurrence, Local obesity disorder breast cancer breast carcinoma psoriasis tuberculosis cancer cutaneous lupus erythematosus interstitial cystitis lung cancer sarcoidosis ulcerative colitis cystic fibrosis depressive disorder endometriosis Neoplasm Recurrence, Local obesity disorder breast cancer breast carcinoma psoriasis tuberculosis cancer cutaneous lupus erythematosus interstitial cystitis lung cancer sarcoidosis ulcerative colitis cystic fibrosis depressive disorder head and neck cancer invasive ductal breast carcinoma lung carcinoma neurodegenerative disease ovarian cancer Sjogren syndrome Crohn disease juvenile dermatomyositis

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.