9DM6 | pdb_00009dm6

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with an ethylhydrazide inhibitor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Arginase/deacetylase-like	8087567	3000260	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Arginase/deacetylase-like	8087567	3000260	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Arginase/deacetylase-like	8087567	3000260	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Arginase/deacetylase-like	8087567	3000260	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C, D	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 [auth B], B [auth A], C, D	Hdac6 protein	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity transition metal ion binding zinc ion binding cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity transition metal ion binding zinc ion binding tubulin 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 histone deacetylase activity	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 macromolecule deacylation protein deacetylation regulation of primary metabolic process regulation of tubulin deacetylation protein deacylation regulation of protein deacetylation tubulin deacetylation macromolecule modification 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 macromolecule deacylation protein deacetylation regulation of primary metabolic process regulation of tubulin deacetylation protein deacylation regulation of protein deacetylation tubulin deacetylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process regulation of metabolic process developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development 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 definitive hemopoiesis cellular developmental process hemopoiesis cell differentiation cell development behavior locomotory behavior swimming behavior hematopoietic progenitor cell differentiation	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D	IPR000286	Histone deacetylase family	Family
A [auth B], B [auth A], C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR023801	Histone deacetylase domain	Domain
A [auth B], B [auth A], C, D	IPR001607	Zinc finger, UBP-type	Domain
A [auth B], B [auth A], C, D	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C, D	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C, D	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.