6WDY

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole Phenylhydroxamate Inhibitor

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Hist_deacetyl	e6wdyA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
A	UNK_F_TYPE	e6wdyA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Polyamine deacetylase HDAC10	deacetylase activity deacylase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding acetylspermidine deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds deacetylase activity deacylase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding acetylspermidine deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds acetylputrescine deacetylase activity	catabolic process macroautophagy autophagy cellular process metabolic process process utilizing autophagic mechanism macromolecule deacylation polyamine metabolic process amine metabolic process spermidine metabolic process polyamine deacetylation spermidine deacetylation macromolecule modification macromolecule metabolic process catabolic process macroautophagy autophagy cellular process metabolic process process utilizing autophagic mechanism macromolecule deacylation polyamine metabolic process amine metabolic process spermidine metabolic process polyamine deacetylation spermidine deacetylation macromolecule modification macromolecule metabolic process biogenic amine metabolic process regulation of biological process regulation of cellular process regulation of protein modification process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein deacetylation regulation of primary metabolic process regulation of tubulin deacetylation protein deacylation regulation of protein deacetylation tubulin deacetylation protein metabolic process protein modification process regulation of metabolic process regulation of biosynthetic process epigenetic regulation of gene expression gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis behavior multicellular organismal process locomotory behavior swimming behavior nucleobase-containing compound metabolic process homologous recombination DNA recombination DNA metabolic process nucleic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000286	Histone deacetylase family	Family
A	IPR023801	Histone deacetylase domain	Domain
A	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
A	IPR050284	Histone deacetylase and polyamine deacetylase	Family

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.