6KBP | pdb_00006kbp

Crystal structure of human D-amino acid oxidase mutant (P219L) complexed with benzoate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Flavoreductase-like	8068931	3000055	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoreductase-like	8068931	3000055	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoreductase-like	8068931	3000055	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoreductase-like	8068931	3000055	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)
D	Ion_trans	e6kbpD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Ion_trans	ECOD (v294.1)
C	Ion_trans	e6kbpC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Ion_trans	ECOD (v294.1)
B	Ion_trans	e6kbpB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Ion_trans	ECOD (v294.1)
A	Ion_trans	e6kbpA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Ion_trans	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
D	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (utative)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
C	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (utative)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
B	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (utative)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
A	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01266	FAD dependent oxidoreductase (DAO)	FAD dependent oxidoreductase	This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	D-amino-acid oxidase	oxidoreductase activity, acting on the CH-NH2 group of donors D-amino-acid dehydrogenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor D-amino-acid oxidase activity primary methylamine oxidase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding oxidoreductase activity, acting on the CH-NH2 group of donors D-amino-acid dehydrogenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor D-amino-acid oxidase activity primary methylamine oxidase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding aliphatic amine oxidase activity glycine oxidase activity aliphatic amine dehydrogenase activity identical protein binding protein binding	dopamine metabolic process catechol-containing compound metabolic process amine metabolic process biogenic amine biosynthetic process biosynthetic process catecholamine metabolic process amine biosynthetic process dopamine biosynthetic process phenol-containing compound metabolic process catecholamine biosynthetic process phenol-containing compound biosynthetic process metabolic process cellular process catechol-containing compound biosynthetic process dopamine metabolic process catechol-containing compound metabolic process amine metabolic process biogenic amine biosynthetic process biosynthetic process catecholamine metabolic process amine biosynthetic process dopamine biosynthetic process phenol-containing compound metabolic process catecholamine biosynthetic process phenol-containing compound biosynthetic process metabolic process cellular process catechol-containing compound biosynthetic process biogenic amine metabolic process neutrophil-mediated killing of symbiont cell biological process involved in interspecies interaction between organisms response to stimulus disruption of cell in another organism defense response to Gram-negative bacterium response to biotic stimulus myeloid leukocyte mediated immunity defense response to bacterium neutrophil mediated immunity response to bacterium response to stress leukocyte mediated immunity response to external biotic stimulus killing of cells of another organism neutrophil-mediated killing of bacterium neutrophil mediated cytotoxicity response to other organism defense response response to external stimulus leukocyte mediated cytotoxicity immune effector process neutrophil-mediated killing of gram-negative bacterium immune system process disruption of anatomical structure in another organism cell killing catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process D-amino acid metabolic process small molecule metabolic process small molecule catabolic process D-amino acid catabolic process amino acid catabolic process D-serine catabolic process L-proline catabolic process L-amino acid catabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid catabolic process L-proline metabolic process D-alanine catabolic process branched-chain amino acid metabolic process L-leucine metabolic process multicellular organismal process digestion	presynapse cellular anatomical structure synapse cell junction presynaptic active zone intracellular anatomical structure cytoplasm cytosol peroxisomal matrix membrane-bounded organelle peroxisome membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen presynapse cellular anatomical structure synapse cell junction presynaptic active zone intracellular anatomical structure cytoplasm cytosol peroxisomal matrix membrane-bounded organelle peroxisome membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle microbody lumen microbody

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023209	D-amino-acid oxidase	Family
A, B, C, D	IPR006181	D-amino acid oxidase, conserved site	Conserved Site
A, B, C, D	IPR006076	FAD dependent oxidoreductase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P14920	schizophrenia amyotrophic lateral sclerosis Liver Cirrhosis, Experimental bipolar disorder glioblastoma malignant ependymoma subependymal giant cell astrocytoma autism bipolar I disorder major affective disorder 2

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.