5EDU

Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Arginase/deacetylase-like	8087569	3000260	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	HDAC-like	8087568	4000427	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Arginase/deacetylase-like	8087569	3000260	SCOP2 (2022-06-29)
B [auth A]	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	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	e5eduB2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
A [auth B]	SBP_bac_1_C,SBP_bac_1_N_2	e5eduB3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C,SBP_bac_1_N_2	ECOD (1.6)
B [auth A]	Hist_deacetyl	e5eduA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
B [auth A]	SBP_bac_1_C,SBP_bac_1_N_2	e5eduA3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C,SBP_bac_1_N_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A]	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A [auth B], B [auth A]	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]	Maltose-binding periplasmic protein, Histone deacetylase 6 chimera	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein binding misfolded protein binding histone deacetylase binding enzyme binding cytoskeletal protein binding tubulin binding transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein binding misfolded protein binding histone deacetylase binding enzyme binding cytoskeletal protein binding tubulin binding alpha-tubulin binding microtubule binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding deacetylase activity tubulin deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity transcription factor binding transcription coregulator binding transcription corepressor binding ubiquitin binding ubiquitin-like protein binding beta-catenin binding tau protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding Hsp90 protein binding heat shock protein binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding actin binding beta-tubulin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding protein-containing complex binding dynein complex binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus regulation of biological process catabolic process regulation of cellular process macroautophagy autophagy biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process cellular response to heat response to heat response to abiotic stimulus response to temperature stimulus positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process positive regulation of cellular process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation macromolecule metabolic process regulation of molecular function regulation of catalytic activity negative regulation of oxidoreductase activity negative regulation of molecular function negative regulation of catalytic activity regulation of oxidoreductase activity regulation of microtubule-based process regulation of microtubule-based movement microtubule-based movement microtubule-based process response to ketone response to lipid response to endogenous stimulus response to alcohol response to glucocorticoid response to corticosterone response to mineralocorticoid response to corticosteroid response to hormone response to steroid hormone response to organic cyclic compound response to dexamethasone cellular component organization cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization or biogenesis developmental process fat cell differentiation regulation of developmental process cellular developmental process regulation of cell differentiation cell differentiation regulation of fat cell differentiation multicellular organismal process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development anatomical structure development dendritic spine morphogenesis synapse organization system development dendritic spine development plasma membrane bounded cell projection organization dendritic spine organization postsynapse organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis cell junction organization neuron development neuron projection organization cellular component biogenesis cellular component assembly aggresome assembly inclusion body assembly cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein response to topologically incorrect protein organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization negative regulation of biological process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process establishment of organelle localization cellular localization organelle transport along microtubule establishment of mitochondrion localization intracellular transport axonal transport mitochondrion localization establishment of mitochondrion localization, microtubule-mediated axo-dendritic transport mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport axonal transport of mitochondrion enucleate erythrocyte maturation erythrocyte development homeostatic process erythrocyte maturation enucleate erythrocyte development myeloid cell homeostasis cell maturation erythrocyte homeostasis enucleation hemopoiesis erythrocyte enucleation developmental maturation erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation anatomical structure maturation immune system process myeloid cell development homeostasis of number of cells enucleate erythrocyte differentiation positive regulation of cell communication signaling modulation of chemical synaptic transmission synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic cell communication synaptic signaling trans-synaptic signaling regulation of signaling positive regulation of synaptic transmission cell-cell signaling positive regulation of synaptic transmission, glutamatergic chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication positive regulation of signaling lysosome localization vacuolar localization regulation of cellular component organization negative regulation of cellular component organization regulation of protein-containing complex disassembly negative regulation of protein-containing complex disassembly negative regulation of proteolysis regulation of proteolysis proteolysis negative regulation of protein metabolic process response to immobilization stress response to growth factor cellular response to parathyroid hormone stimulus cellular response to endogenous stimulus response to parathyroid hormone cellular response to hormone stimulus response to amine response to nitrogen compound response to amphetamine intracellular receptor signaling pathway regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction regulation of intracellular signal transduction regulation of intracellular steroid hormone receptor signaling pathway signal transduction androgen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to organic cyclic compound regulation of androgen receptor signaling pathway regulation of response to stimulus cellular response to lipid nuclear receptor-mediated signaling pathway positive regulation of nervous system development regulation of neurogenesis regulation of cell morphogenesis regulation of cell development positive regulation of developmental process regulation of dendrite morphogenesis positive regulation of cell projection organization regulation of cell projection organization positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process regulation of neuron projection development positive regulation of cellular component organization regulation of nervous system development positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of dendrite morphogenesis regulation of plasma membrane bounded cell projection organization proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process protein quality control for misfolded or incompletely synthesized proteins regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization negative regulation of microtubule depolymerization microtubule cytoskeleton organization microtubule polymerization or depolymerization regulation of microtubule depolymerization negative regulation of supramolecular fiber organization negative regulation of microtubule polymerization or depolymerization regulation of protein depolymerization negative regulation of cytoskeleton organization regulation of organelle organization negative regulation of protein depolymerization negative regulation of organelle organization microtubule depolymerization regulation of supramolecular fiber organization protein depolymerization regulation of microtubule cytoskeleton organization positive regulation of locomotion regulation of cell motility positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration epithelial cell migration regulation of epithelial cell migration epithelium migration regulation of locomotion protein acylation negative regulation of protein modification process negative regulation of protein acetylation regulation of protein acetylation protein acetylation regulation of autophagy of mitochondrion autophagy of mitochondrion protein destabilization regulation of protein stability regulation of biological quality peptidyl-lysine deacetylation peptidyl-lysine modification macromolecule deacylation protein deacetylation protein deacylation protein localization regulation of localization establishment of protein localization regulation of protein localization regulation of establishment of protein localization regulation of cellular localization cellular macromolecule localization modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process epigenetic regulation of gene expression chromatin organization chromatin remodeling negative regulation of locomotion developmental growth negative regulation of chemotaxis negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of response to external stimulus cell growth negative regulation of neurogenesis regulation of axon extension involved in axon guidance regulation of extent of cell growth negative regulation of nervous system development negative regulation of cell differentiation neuron projection extension regulation of developmental growth developmental cell growth negative regulation of developmental process growth axon development negative regulation of axon extension regulation of chemotaxis regulation of cell growth negative regulation of cell development neuron projection guidance axon extension regulation of growth axonogenesis regulation of cellular component size negative regulation of growth neuron projection extension involved in neuron projection guidance negative regulation of axon extension involved in axon guidance negative regulation of cell growth developmental growth involved in morphogenesis negative regulation of response to external stimulus regulation of axon extension regulation of axonogenesis axon extension involved in axon guidance negative regulation of cell projection organization regulation of cell size negative regulation of response to stimulus axon guidance negative regulation of neuron projection development regulation of anatomical structure size regulation of cellular component biogenesis negative regulation of protein-containing complex assembly regulation of protein-containing complex assembly protein-containing complex assembly positive regulation of signaling receptor activity regulation of signaling receptor activity positive regulation of molecular function protein polyubiquitination protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal mitophagy type 2 mitophagy organelle disassembly cilium disassembly cilium organization nitrogen compound transport misfolded protein transport polyubiquitinated misfolded protein transport protein transport polyubiquitinated protein transport intracellular protein transport negative regulation of catabolic process negative regulation of aggrephagy regulation of aggrephagy negative regulation of macroautophagy negative regulation of autophagy aggrephagy reactive oxygen species metabolic process hydrogen peroxide metabolic process negative regulation of reactive oxygen species metabolic process negative regulation of hydrogen peroxide metabolic process regulation of hydrogen peroxide metabolic process regulation of reactive oxygen species metabolic process tubulin deacetylation negative regulation of gene expression negative regulation of gene expression, epigenetic organelle assembly plasma membrane bounded cell projection assembly cilium assembly cell projection assembly collateral sprouting cellular response to oxidative stress cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species positive regulation of cellular response to oxidative stress regulation of cellular response to stress regulation of cellular response to oxidative stress positive regulation of response to stimulus regulation of response to stress regulation of response to oxidative stress positive regulation of response to oxidative stress positive regulation of protein deacetylation positive regulation of tubulin deacetylation regulation of protein deacetylation regulation of tubulin deacetylation cholangiocyte proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cholangiocyte proliferation regulation of cell population proliferation positive regulation of cholangiocyte proliferation regulation of epithelial cell proliferation epithelial cell proliferation	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope somatodendritic compartment cell body perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol cell leading edge inclusion body membrane-bounded organelle intracellular membraneless organelle cilium plasma membrane bounded cell projection intracellular organelle ciliary basal body cell projection microtubule organizing center cytoskeleton organelle membraneless organelle microtubule cytoskeleton neuron projection cytoplasm axon axon cytoplasm neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm membrane microdomain membrane raft plasma membrane raft plasma membrane region caveola catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex nucleoplasm organelle lumen nuclear lumen dendrite dendritic tree perinuclear region of cytoplasm microtubule associated complex polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex centrosome aggresome endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome multivesicular body vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A [auth B], B [auth A]	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A [auth B], B [auth A]	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A [auth B], B [auth A]	IPR000286	Histone deacetylase family	Family
A [auth B], B [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth B], B [auth A]	IPR023801	Histone deacetylase domain	Domain
A [auth B], B [auth A]	IPR001607	Zinc finger, UBP-type	Domain
A [auth B], B [auth A]	IPR050284	Histone deacetylase and polyamine deacetylase	Family
A [auth B], B [auth A]	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth A]	Pharos: Q9UBN7	X-linked dominant chondrodysplasia, Chassaing-Lacombe type melanoma prostate cancer astrocytic tumor hydrocephalus malignant colon neoplasm medulloblastoma oligodendroglioma ovarian neoplasm cutaneous melanoma intellectual disability Malignant neoplasm of ovary osteosarcoma plasma cell myeloma depressive disorder X-linked dominant chondrodysplasia, Chassaing-Lacombe type melanoma prostate cancer astrocytic tumor hydrocephalus malignant colon neoplasm medulloblastoma oligodendroglioma ovarian neoplasm cutaneous melanoma intellectual disability Malignant neoplasm of ovary osteosarcoma plasma cell myeloma depressive disorder lung cancer mature T-cell and NK-cell non-Hodgkin lymphoma ovarian cancer primary cutaneous T-cell lymphoma

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.