3L6B

X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3l6ba_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	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)
A	SCOP2 Family	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8066142	4000798	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8066143	3001427	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PALP	e3l6bA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	Serine racemase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding organic cyclic compound binding anion binding heterocyclic compound binding protein binding PDZ domain binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding organic cyclic compound binding anion binding heterocyclic compound binding protein binding PDZ domain binding protein domain specific binding racemase activity, acting on amino acids and derivatives 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 organic cyclic compound serine family amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process L-serine metabolic process biological process involved in interspecies interaction between organisms response to lipid response to other organism response to oxygen-containing compound 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	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
A	IPR000634	Serine/threonine dehydratase, pyridoxal-phosphate-binding site	Binding Site
A	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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.