3ANV | pdb_00003anv

Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3anva1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Alanine racemase-like, C-terminal domain	D-serine dehydratase	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
A	d3anva2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	D-serine dehydratase	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YjeF_N	e3anvA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.37.20	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
A	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14031	Putative serine dehydratase domain (D-ser_dehydrat)	Putative serine dehydratase domain	This domain is found at the C-terminus of yeast D-serine dehydratase [1]. Structures have been solved for two bacterial members of this family. The yeast protein has been shown to be a zinc dependent enzyme.	Domain
A	PF01168	Alanine racemase, N-terminal domain (Ala_racemase_N)	Alanine racemase, N-terminal domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	D-serine dehydratase	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding D-serine ammonia-lyase activity lyase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding D-serine ammonia-lyase activity lyase activity ammonia-lyase activity catalytic activity carbon-nitrogen lyase activity	catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process D-serine 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 catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process D-serine 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 metabolic process cellular process small molecule metabolic process small molecule catabolic process D-amino acid catabolic process amino acid catabolic process D-serine catabolic process	somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029066	PLP-binding barrel	Homologous Superfamily
A	IPR042208	D-serine dehydratase-like domain superfamily	Homologous Superfamily
A	IPR026956	D-serine dehydratase-like domain	Domain
A	IPR051466	D-amino acid metabolism enzyme	Family
A	IPR001608	Alanine racemase, N-terminal	Domain

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.