5G0I

Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with Nexturastat A

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5g0ia1	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	ZEBRAFISH (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
B	d5g0ib1	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	SCOP2B Superfamily	Arginase/deacetylase-like	8087567	3000260	SCOP2B (2022-06-29)
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	Hist_deacetyl	e5g0iA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
B	Hist_deacetyl	e5g0iB1	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	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
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, 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
A, B	HDAC6	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 hydrolase 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 hydrolase 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, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity histone modifying activity	regulation of biological process organonitrogen compound metabolic 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 organic substance metabolic process regulation of protein deacetylation tubulin deacetylation regulation of biological process organonitrogen compound metabolic 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 organic substance metabolic process regulation of protein deacetylation tubulin deacetylation macromolecule modification metabolic 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 definitive hemopoiesis cellular developmental process hemopoiesis cell differentiation cell development cellular process behavior locomotory behavior swimming behavior hematopoietic progenitor cell differentiation regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle 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 cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	histone deacetylase 6 enzyme (HDAC6) M-CSA #998	Histone deacetylase 6 enzyme (HDAC6) is a metalloenzyme, part of the HDAC family. The HDAC family includes 18 isoforms which are grouped into four classes (I, II, III, and IV). HDACs in class III use an NAD⁺ cofactor, whilst the others are metalloenzymes which use a Zn(II) metal ion centre. HDAC6 is in class II and is involved in the maintenance of a cell's shape and its polarity during cell division and migration, intracellular transport and angiogenesis. HDACs catalyse the removal of the acyl group from a lysine amino acid of the substrate of nuclear and cytosol proteins. In general, protein acylation and deacylation processes are a key part of cell cycle regulation. HDAC6 has a heterodimeric structure with two different catalytic domains, CD1 and CD2. The domains present a similar structure but show differing substrate specificities and their roles remain unclear. HDAC6 is of interest for its role in the fight against cancer and various other pathologies.	Defined by 7 residues: HIS:A-170 [auth A-192]HIS:A-171 [auth A-193]ASP:A-206 [auth A-228]ASP:A-208 [auth A-230]HIS:A-210 [auth A-232]ASP:A-301 [auth A-323]TYR:A-341 [auth A-363] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.