3K5T | pdb_00003k5t

Crystal structure of human diamine oxidase in space group C2221

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cu_amine_oxid	e3k5tA4	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Cu_amine_oxid	ECOD (1.6)
A	Cu_amine_oxidN2	e3k5tA6	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN2	ECOD (1.6)
A	Cu_amine_oxidN3	e3k5tA5	A: a+b two layers	X: Cystatin-like	H: Amine oxidase N-terminal region (From Topology)	T: Amine oxidase N-terminal region	F: Cu_amine_oxidN3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.450.40	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	2.70.98.20	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02728	Copper amine oxidase, N3 domain (Cu_amine_oxidN3)	Copper amine oxidase, N3 domain	This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quino ...	This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).	Domain
A	PF02727	Copper amine oxidase, N2 domain (Cu_amine_oxidN2)	Copper amine oxidase, N2 domain	This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quino ...	This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).	Domain
A	PF01179	Copper amine oxidase, enzyme domain (Cu_amine_oxid)	Copper amine oxidase, enzyme domain	Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dime ...	Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Diamine oxidase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor putrescine oxidase activity diamine oxidase activity catalytic activity transition metal ion binding copper ion binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor putrescine oxidase activity diamine oxidase activity catalytic activity transition metal ion binding copper ion binding identical protein binding protein binding protein homodimerization activity protein dimerization activity histamine oxidase activity quinone binding primary methylamine oxidase activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	amine metabolic process putrescine metabolic process metabolic process cellular process polyamine metabolic process biogenic amine metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane intracellular organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane intracellular organelle intracellular anatomical structure peroxisome microbody cytoplasm intracellular membrane-bounded organelle cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen endomembrane system intracellular organelle lumen cytoplasmic vesicle organelle lumen specific granule lumen secretory granule secretory vesicle specific granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036460	Copper amine oxidase, catalytic domain superfamily	Homologous Superfamily
A	IPR015798	Copper amine oxidase, catalytic domain	Domain
A	IPR015802	Copper amine oxidase, N3-terminal	Domain
A	IPR000269	Copper amine oxidase	Family
A	IPR049947	Copper amine oxidase, copper-binding site	Conserved Site
A	IPR016182	Copper amine oxidase, N-terminal	Homologous Superfamily
A	IPR049948	Copper amine oxidase, TPQ-binding site	Conserved Site
A	IPR015800	Copper amine oxidase, N2-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P19801	Cardiomegaly hypertensive disorder pneumocystosis atopic eczema human African trypanosomiasis lung cancer metabolic syndrome X ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis Barrett esophagus carpal tunnel syndrome malignant colon neoplasm nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma Cardiomegaly hypertensive disorder pneumocystosis atopic eczema human African trypanosomiasis lung cancer metabolic syndrome X ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis Barrett esophagus carpal tunnel syndrome malignant colon neoplasm nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma esophageal adenocarcinoma interstitial cystitis malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	TPQ	Parent Component: TYR RESID: AA0147 PSI-MOD : oxidation of tyrosine to L-2',4',5'-topaquinone MOD:00156

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.