7NBG | pdb_00007nbg

Crystal structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen.

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth DDD]	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8066143	3001427	SCOP2B (2022-06-29)
C [auth CCC]	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8066143	3001427	SCOP2B (2022-06-29)
B [auth BBB]	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8066143	3001427	SCOP2B (2022-06-29)
A [auth AAA]	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8066143	3001427	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 [auth DDD]	Omp85	e7nbgDDD1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
C [auth CCC]	Omp85	e7nbgCCC1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
B [auth BBB]	Omp85	e7nbgBBB1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
A [auth AAA]	Omp85	e7nbgAAA1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	Serine racemase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding protein binding PDZ domain binding protein domain specific binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding anion binding heterocyclic compound binding protein binding PDZ domain binding protein domain specific binding isomerase activity racemase and epimerase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity catalytic activity threonine racemase activity serine racemase activity magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding carbohydrate derivative binding ribonucleotide binding organic acid binding glycine binding amino acid binding carboxylic acid binding identical protein binding protein homodimerization activity protein dimerization activity L-serine ammonia-lyase activity lyase activity ammonia-lyase activity carbon-nitrogen lyase activity D-serine ammonia-lyase activity	response to stimulus response to chemical response to xenobiotic stimulus oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process D-serine metabolic process alpha-amino acid metabolic process D-serine biosynthetic process carboxylic acid biosynthetic process response to stimulus response to chemical response to xenobiotic stimulus oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process D-serine metabolic process alpha-amino acid metabolic process D-serine biosynthetic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process D-amino acid biosynthetic process D-amino acid metabolic process metabolic process cellular process small molecule metabolic process alpha-amino acid biosynthetic process non-proteinogenic amino acid biosynthetic process response to ketone response to oxygen-containing compound response to nitrogen compound response to ketamine L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process biological process involved in interspecies interaction between organisms response to lipid response to other organism response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin pyruvate metabolic process monocarboxylic acid biosynthetic process pyruvate biosynthetic process monocarboxylic acid metabolic process	cellular anatomical structure apical part of cell intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR000634	Serine/threonine dehydratase, pyridoxal-phosphate-binding site	Binding Site
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	Pharos: Q9GZT4	Liver Cirrhosis, Experimental squamous cell carcinoma autism spectrum disorder heart disease lung adenocarcinoma maturity-onset diabetes of the young pancreatic intraductal papillary-mucinous carcinoma psoriasis type 2 diabetes mellitus adenoma carcinoma of esophagus large cell medulloblastoma lung cancer medulloblastoma pancreatic intraductal papillary-mucinous neoplasm Liver Cirrhosis, Experimental squamous cell carcinoma autism spectrum disorder heart disease lung adenocarcinoma maturity-onset diabetes of the young pancreatic intraductal papillary-mucinous carcinoma psoriasis type 2 diabetes mellitus adenoma carcinoma of esophagus large cell medulloblastoma lung cancer medulloblastoma pancreatic intraductal papillary-mucinous neoplasm schizophrenia attention deficit hyperactivity disorder, inattentive type malignant ependymoma osteosarcoma pituitary cancer

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.