9CBK | pdb_00009cbk

Crystal Structure of Danio rerio Histone Deacetylase 6 in Complex with p-Aminomethyl Phenylthioketone

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8087565	3000260	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Arginase/deacetylase-like	8087565	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)
B	Reovirus_L2_GTase	e9cbkB1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Reovirus_L2_GTase	ECOD (v295)
A	Reovirus_L2_GTase	e9cbkA1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Reovirus_L2_GTase	ECOD (v295)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, 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 transferase activity cytoskeletal protein 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 transferase activity cytoskeletal protein binding actin binding protein binding 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	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 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 cellular component organization regulation of biological process regulation of cellular process regulation of cellular component organization negative regulation of cellular component organization negative regulation of cellular process biological regulation negative regulation of biological process cellular process cellular component organization or biogenesis response to stimulus response to stress behavior locomotory behavior swimming behavior RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process regulation of protein modification process regulation of protein 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 protein metabolic process protein modification process regulation of metabolic process localization mitochondrion localization organelle localization positive regulation of cellular component organization positive regulation of biological process positive regulation of cellular process definitive hemopoiesis cellular developmental process hemopoiesis cell differentiation cell development hematopoietic progenitor cell differentiation regulation of microtubule-based process microtubule-based process chromatin organization	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection axon membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

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

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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.