3PHD | pdb_00003phd

Crystal structure of human HDAC6 in complex with ubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d3phdf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	ChapFlgA	e3phdH1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: ChapFlgA	ECOD (v294.1)
G	AAA	e3phdG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
D	V-set	e3phdD2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (v294.1)
C	V-set	e3phdC2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (v294.1)
B	AAA	e3phdB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
A	AAA	e3phdA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
E, F, G, H	Polyubiquitin	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process regulation of biological process neuron apoptotic process regulation of cellular process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process multicellular organismal-level homeostasis homeostatic process energy homeostasis regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death positive regulation of intracellular signal transduction signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development forebrain neuron differentiation sexual reproduction organelle fission meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation nuclear division organelle organization meiosis I meiosis I cell cycle process female meiosis I female meiotic nuclear division meiotic nuclear division cell cycle cell cycle process positive regulation of protein monoubiquitination protein monoubiquitination regulation of protein monoubiquitination proteasomal protein catabolic process regulation of catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process male meiosis I male meiotic nuclear division male gamete generation connective tissue development adipose tissue development fat pad development tissue development female gonad development female sex differentiation development of primary female sexual characteristics establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle endosome membrane endosome mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body
A, B, C, D	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 ATPase regulator activity deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity protein binding binding misfolded protein binding histone deacetylase binding enzyme binding molecular function inhibitor activity molecular function regulator activity ATPase inhibitor activity ATPase regulator 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 localization regulation of localization establishment of protein localization regulation of protein localization macromolecule localization regulation of establishment of protein localization intracellular protein localization establishment of localization 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 primary metabolic process protein catabolic process macromolecule catabolic process 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 protein metabolic process macromolecule metabolic process 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 protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 cellular component disassembly protein-containing complex disassembly protein deacylation macromolecule deacylation protein deacetylation 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 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 RNA metabolic process regulation of primary 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 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 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 transport 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 organelle disassembly cilium disassembly cilium organization 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 lysosome localization vacuolar localization regulation of protein-containing complex disassembly negative regulation of protein-containing complex disassembly tubulin deacetylation 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 axonogenesis developmental growth cell growth collateral sprouting developmental cell growth growth axon development developmental growth involved in morphogenesis 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 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 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 intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear protein-containing complex histone deacetylase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR019954	Ubiquitin conserved site	Conserved Site
E, F, G, H	IPR050158	Ubiquitin and ubiquitin-like	Family
E, F, G, H	IPR000626	Ubiquitin-like domain	Domain
E, F, G, H	IPR019956	Ubiquitin domain	Domain
E, F, G, H	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR023801	Histone deacetylase domain	Domain
A, B, C, D	IPR001607	Zinc finger, UBP-type	Domain
A, B, C, D	IPR000286	Histone deacetylase HDAC	Family
A, B, C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A, B, C, D	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: P0CG47	astrocytic tumor cleft soft palate lung cancer Cleft of hard palate ovarian cancer isolated cleft palate
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.