4WPH

Crystal structure of USP7 ubiquitin-like domains in compact conformation

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	USP7_ICP0_bdg_1st	e4wphA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: USP7_ICP0_bdg_1st	ECOD (1.6)
A	USP7_ICP0_bdg_3rd	e4wphA3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: USP7_ICP0_bdg_3rd	ECOD (1.6)
A	USP7_ICP0_bdg_2nd	e4wphA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: USP7_ICP0_bdg_2nd	ECOD (1.6)
B	USP7_ICP0_bdg_1st	e4wphB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: USP7_ICP0_bdg_1st	ECOD (1.6)
B	USP7_ICP0_bdg_3rd	e4wphB3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: USP7_ICP0_bdg_3rd	ECOD (1.6)
B	USP7_ICP0_bdg_2nd	e4wphB2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: USP7_ICP0_bdg_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12436	ICP0-binding domain of Ubiquitin-specific protease 7 (USP7_ICP0_bdg)	ICP0-binding domain of Ubiquitin-specific protease 7	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	ICP0	DNA binding binding organic cyclic compound binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity cation binding DNA binding binding organic cyclic compound binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity cation binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to peptide response to chemical immune system process defense response to other organism response to stress innate immune response biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to peptide response to chemical immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus response to type I interferon protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell PML body disruption of anatomical structure in another organism symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host defense response response to host defenses symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated perturbation of host ubiquitin-like protein modification symbiont-mediated perturbation of host exit from mitosis symbiont-mediated perturbation of host cell cycle progression latent virus replication viral latency viral process release from viral latency multicellular organismal process regulation of cellular process negative regulation of biological process modulation by virus of host process symbiont-mediated suppression of host gene expression cytokine production regulation of biological process type I interferon production negative regulation of metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process symbiont-mediated perturbation of host gene expression negative regulation of multicellular organismal process regulation of metabolic process virus-mediated perturbation of host defense response perturbation by virus of host immune response suppression by virus of host type I interferon production negative regulation of type I interferon production negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process modulation by virus of host cellular process regulation of biosynthetic process suppression by virus of host cytokine production biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of biosynthetic process modulation by virus of host cytokine production symbiont-mediated suppression of host cytokine production regulation of type I interferon production catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of protein metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process	virion component viral tegument host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus host intracellular organelle host cell cytoplasm
A, B	Ubiquitin carboxyl-terminal hydrolase 7	p53 binding protein binding binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity K48-linked deubiquitinase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity cysteine-type deubiquitinase activity	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary 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 regulation of molecular function biosynthetic process regulation of DNA-binding transcription factor activity metabolic process cellular process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process regulation of protein stability regulation of biological quality protein stabilization negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic rhythmic process circadian rhythm regulation of circadian rhythm regulation of localization cellular localization regulation of transport transport intracellular transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport endosomal transport localization regulation of cellular localization cytosolic transport establishment of localization in cell retrograde transport, endosome to Golgi regulation of retrograde transport, endosome to Golgi regulation of intracellular transport protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein deubiquitination monoubiquitinated protein deubiquitination protein modification by small protein removal cellular response to stimulus response to stimulus DNA metabolic process DNA alkylation repair cellular response to stress DNA damage response response to stress DNA repair transcription-coupled nucleotide-excision repair nucleotide-excision repair negative regulation of DNA-binding transcription factor activity negative regulation of NF-kappaB transcription factor activity negative regulation of molecular function catabolic process negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process negative regulation of protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis negative regulation of protein metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process establishment of protein localization to telomere protein localization establishment of protein localization regulation of protein localization regulation of protein localization to chromosome, telomeric region cellular macromolecule localization establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization protein localization to chromosome, telomeric region establishment of protein localization to organelle protein localization to chromosome regulation of establishment of protein localization to telomere macromolecule localization protein localization to organelle symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host cell PML body disruption of anatomical structure in another organism symbiont-mediated disruption of host cellular anatomical structure regulation of telomere maintenance regulation of cellular component organization telomere organization chromosome organization regulation of chromosome organization regulation of organelle organization telomere maintenance organelle organization telomere capping regulation of telomere capping regulation of DNA metabolic process signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling signal transduction regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling monosaccharide metabolic process negative regulation of small molecule metabolic process gluconeogenesis negative regulation of gluconeogenesis regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process negative regulation of carbohydrate metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process regulation of gluconeogenesis regulation of carbohydrate biosynthetic process glucose metabolic process signal transduction by p53 class mediator regulation of signal transduction by p53 class mediator	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex membraneless organelle intracellular membraneless organelle chromosome nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR018957	Zinc finger, C3HC4 RING-type	Domain
C, D	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C, D	IPR001841	Zinc finger, RING-type	Domain
A, B	IPR028889	Ubiquitin specific protease domain	Domain
A, B	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B	IPR024729	Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain	Domain
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR002083	MATH/TRAF domain	Domain
A, B	IPR029346	Ubiquitin carboxyl-terminal hydrolase, C-terminal	Domain
A, B	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
A, B	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B	IPR008974	TRAF-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q93009	urinary bladder cancer prostate cancer Hao-Fountain syndrome Prostatic Neoplasms intellectual disability urinary bladder neoplasm

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.