5EFK

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (Y745F mutant) in complex with alpha tubulin K40 tripeptide substrate

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d5efkb_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)

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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	Hist_deacetyl	e5efkB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	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
B [auth A]	alpha tubulin K40 tripeptide	-	-	-
A [auth B]	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 multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis 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]	IPR000286	Histone deacetylase family	Family
A [auth B]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth B]	IPR023801	Histone deacetylase domain	Domain
A [auth B]	IPR001607	Zinc finger, UBP-type	Domain
A [auth B]	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A [auth B]	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
A [auth B]	IPR050284	Histone deacetylase and polyamine deacetylase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth A]	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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.