1VKH | pdb_00001vkh

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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	alpha/beta-Hydrolases	8041382	3000102	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Chal_sti_synt_N	e1vkhB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Chal_sti_synt_N	ECOD (v294.1)
A	Abhydrolase_3, Say1_Mug180	e1vkhA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: Abhydrolase_3, Say1_Mug180	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
A	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 growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process 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 growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process 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 oxoacid metabolic process NAD+ biosynthetic process nucleotide biosynthetic process indole-containing compound metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process L-tryptophan metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process aromatic amino acid metabolic process pyridine-containing compound biosynthetic process carboxylic acid metabolic process 'de novo' NAD+ biosynthetic process from L-tryptophan primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process L-amino acid metabolic process purine-containing compound metabolic process nicotinamide nucleotide biosynthetic process proteinogenic amino acid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process purine nucleotide biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027519	Kynurenine formamidase, vertebrates/fungi-type	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.