1VKH

CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vkha1	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	Putative serine hydrolase Ydr428c	Putative serine hydrolase Ydr428c	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1vkha2	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1vkhb_	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	Putative serine hydrolase Ydr428c	Putative serine hydrolase Ydr428c	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Putative serine hydrolase Ydr428c	8029003	4002295	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta-Hydrolases	8041382	3000102	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	alpha/beta-Hydrolases	8041382	3000102	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)
A	Hydrolase_4	e1vkhA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4	ECOD (1.6)
B	Hydrolase_4	e1vkhB1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
B	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07859	alpha/beta hydrolase fold (Abhydrolase_3)	alpha/beta hydrolase fold	This catalytic domain is found in a very wide range of enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	putative serine hydrolase	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity arylformamidase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process catabolic process oxoacid metabolic process aromatic amino acid family catabolic process indole-containing compound metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process cellular ketone metabolic process carboxylic acid catabolic process indolalkylamine metabolic process small molecule metabolic process amino acid catabolic process aromatic amino acid metabolic process benzene-containing compound metabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process amine metabolic process kynurenine metabolic process tryptophan catabolic process to kynurenine alpha-amino acid catabolic process indole-containing compound catabolic process tryptophan catabolic process metabolic process small molecule catabolic process biogenic amine metabolic process nucleotide biosynthetic process NAD metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process phosphorus metabolic process pyridine nucleotide metabolic process NAD biosynthetic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyridine-containing compound biosynthetic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nicotinamide nucleotide biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process purine nucleotide biosynthetic process 'de novo' NAD biosynthetic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process tryptophan metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process 'de novo' NAD biosynthetic process from tryptophan	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027519	Kynurenine formamidase, vertebrates/fungi-type	Family
A, B	IPR050300	GDXG lipolytic enzyme	Family
A, B	IPR013094	Alpha/beta hydrolase fold-3	Domain
A, B	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily

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.