6CGP | pdb_00006cgp

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with MAIP-032

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6cgpa_	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	SCOP2 Family	HDAC-like	8087564	4000427	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginase/deacetylase-like	8087565	3000260	SCOP2 (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	NNMT_PNMT_TEMT	e6cgpA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: NNMT_PNMT_TEMT	ECOD (v294.1)

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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 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	IPR023801	Histone deacetylase domain	Domain
A	IPR001607	Zinc finger, UBP-type	Domain
A	IPR000286	Histone deacetylase HDAC	Family
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

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.