5GG4 | pdb_00005gg4

Crystal structure of USP7 with RNF169 peptide

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)
D	TTL, ATPgrasp_YheCD	e5gg4D1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Nucleic acid-binding protein	T: Chelatase-like	F: TTL, ATPgrasp_YheCD	ECOD (v294.1)
C	TTL, ATPgrasp_YheCD	e5gg4C1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Nucleic acid-binding protein	T: Chelatase-like	F: TTL, ATPgrasp_YheCD	ECOD (v294.1)
B	TTL, ATPgrasp_YheCD	e5gg4B1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Nucleic acid-binding protein	T: Chelatase-like	F: TTL, ATPgrasp_YheCD	ECOD (v294.1)
A	TTL, ATPgrasp_YheCD	e5gg4A1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Nucleic acid-binding protein	T: Chelatase-like	F: TTL, ATPgrasp_YheCD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
A	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, C, D	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
E, F, G, H	Peptide from E3 ubiquitin-protein ligase RNF169	ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity protein-containing complex binding chromatin binding nucleosome binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process recombinational repair metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of DNA repair regulation of response to stimulus negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol site of double-strand break site of DNA damage chromosome nuclear body nucleoplasm
A, B, C, D	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 protein stability biological regulation regulation of biological quality protein stabilization regulation of cellular process 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 regulation of biosynthetic process regulation of protein stability biological regulation regulation of biological quality protein stabilization regulation of cellular process 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 regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process 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 intercellular transport 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 primary metabolic process 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 nucleic acid metabolic process nucleobase-containing compound 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 catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process negative regulation of protein catabolic process modification-dependent macromolecule catabolic process 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 establishment of protein localization regulation of protein localization regulation of establishment of protein localization establishment of protein localization to organelle regulation of establishment of protein localization to telomere macromolecule localization establishment of protein localization to chromosome intracellular protein localization regulation of establishment of protein localization to chromosome 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 regulation of nucleobase-containing compound metabolic process 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 proteolysis	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
E, F, G, H	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
E, F, G, H	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
E, F, G, H	IPR051657	RNF168/RNF169 E3 ubiquitin-protein ligase	Family
E, F, G, H	IPR001841	Zinc finger, RING-type	Domain
A, B, C, D	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B, C, D	IPR024729	Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain	Domain
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR002083	MATH/TRAF domain	Domain
A, B, C, D	IPR029346	Ubiquitin carboxyl-terminal hydrolase, C-terminal	Domain
A, B, C, D	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
A, B, C, D	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, B, C, D	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B, C, D	IPR008974	TRAF-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: Q8NCN4	colorectal adenoma ovarian cancer colorectal cancer spina bifida osteosarcoma
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.