Annotations: 8G45

Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	z-alpha	e8g45A1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: z-alpha	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02148	Zn-finger in ubiquitin-hydrolases and other protein (zf-UBP)	Zn-finger in ubiquitin-hydrolases and other protein		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone deacetylase 6	protein binding binding misfolded protein binding histone deacetylase binding enzyme binding molecular function inhibitor activity molecular function regulator activity ATPase inhibitor activity deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity enzyme regulator activity protein binding binding misfolded protein binding histone deacetylase binding enzyme binding molecular function inhibitor activity molecular function regulator activity ATPase inhibitor activity deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity enzyme regulator activity peroxidase inhibitor activity enzyme inhibitor activity aminoacyltransferase activity ubiquitin-like protein transferase activity acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity ubiquitin-protein transferase activity cytoskeletal protein binding tubulin binding alpha-tubulin binding microtubule binding tau protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase 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 histone modifying activity transcription factor binding transcription coregulator binding transcription corepressor 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding ubiquitin binding ubiquitin-like protein binding actin binding beta-catenin 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	regulation of biological process catabolic process regulation of cellular process autophagy biological regulation regulation of catabolic process regulation of autophagy cellular process metabolic process regulation of autophagy of mitochondrion process utilizing autophagic mechanism regulation of metabolic process autophagy of mitochondrion protein destabilization regulation of biological process catabolic process regulation of cellular process autophagy biological regulation regulation of catabolic process regulation of autophagy cellular process metabolic process regulation of autophagy of mitochondrion process utilizing autophagic mechanism regulation of metabolic process autophagy of mitochondrion protein destabilization regulation of protein stability regulation of biological quality macroautophagy regulation of macroautophagy cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of type 2 mitophagy positive regulation of type 2 mitophagy positive regulation of biological process positive regulation of autophagy of mitochondrion positive regulation of metabolic process mitophagy positive regulation of macroautophagy positive regulation of cellular process positive regulation of autophagy positive regulation of mitophagy regulation of mitophagy positive regulation of catabolic process type 2 mitophagy regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization negative regulation of biological process regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly negative regulation of cellular process cellular component organization or biogenesis regulation of microtubule-based process regulation of microtubule-based movement microtubule-based movement microtubule-based process 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 macromolecule metabolic process cell surface receptor signaling pathway signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication ERBB signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway protein deacylation macromolecule modification protein metabolic process macromolecule deacylation protein modification process protein deacetylation aggresome assembly inclusion body assembly response to misfolded protein response to topologically incorrect protein regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic 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 regulation of macromolecule metabolic process regulation of gene expression 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 transport establishment of mitochondrion localization intracellular transport axonal transport establishment of localization localization 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 cellular component disassembly organelle organization plasma membrane bounded cell projection organization organelle disassembly cell projection organization cilium disassembly cilium organization establishment of protein localization misfolded protein transport polyubiquitinated misfolded protein transport protein transport macromolecule localization intracellular protein localization 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 lysosome localization vacuolar localization protein-containing complex disassembly regulation of protein-containing complex disassembly negative regulation of protein-containing complex disassembly tubulin deacetylation cellular response to topologically incorrect protein negative regulation of proteolysis regulation of protein metabolic process regulation of proteolysis proteolysis negative regulation of protein metabolic process chromatin organization chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic organelle assembly plasma membrane bounded cell projection assembly cilium assembly cell projection assembly cellular response to oxidative stress response to oxygen-containing compound 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 cellular response to chemical stimulus response to chemical positive regulation of cellular component organization positive regulation of cellular component biogenesis regulation of protein oligomerization positive regulation of protein-containing complex assembly positive regulation of protein oligomerization protein complex oligomerization intracellular receptor signaling pathway response to lipid regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway 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 hormone stimulus regulation of signaling response to endogenous stimulus regulation of androgen receptor signaling pathway regulation of response to stimulus cellular response to lipid regulation of cell communication nuclear receptor-mediated signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of intracellular estrogen receptor signaling pathway positive regulation of response to stimulus regulation of intracellular estrogen receptor signaling pathway positive regulation of intracellular signal transduction estrogen receptor signaling pathway positive regulation of intracellular steroid hormone receptor signaling pathway positive regulation of signaling protein catabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process multicellular organismal process 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 cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol cell leading edge cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol cell leading edge cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection inclusion body perinuclear region of cytoplasm axon intracellular organelle protein-containing complex cytoskeleton organelle membraneless organelle microtubule associated complex intracellular membraneless organelle microtubule cytoskeleton cytoplasmic ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-bounded organelle cilium ciliary basal body microtubule organizing center polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex neuron projection cytoplasm axon cytoplasm centrosome membrane microdomain cell periphery membrane raft plasma membrane raft membrane plasma membrane plasma membrane region caveola aggresome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system cytoplasmic vesicle late endosome multivesicular body vesicle nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular organelle lumen histone deacetylase complex nucleoplasm organelle lumen nuclear lumen

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: 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

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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.