5XVE

Crystal structure of human USP2 C276S mutant in complex with ubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d5xvea_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Ubiquitin carboxyl-terminal hydrolase, UCH	Ubiquitin carboxyl-terminal hydrolase 2, USP2	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5xveb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cysteine proteinases	8033152	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8098884	3000157	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	UCH	e5xveA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
B	ubiquitin_1	e5xveB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family
B	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin carboxyl-terminal hydrolase 2	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity protein binding binding cyclin binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity ubiquitin protein ligase binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity protein binding binding cyclin binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding ion binding metal ion binding small molecule binding identical protein binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process muscle structure development animal organ development anatomical structure development muscle organ development regulation of biosynthetic process rhythmic process regulation of biological process regulation of cellular process circadian regulation of gene expression regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process muscle structure development animal organ development anatomical structure development muscle organ development regulation of biosynthetic process rhythmic process regulation of biological process regulation of cellular process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process response to light stimulus entrainment of circadian clock response to stimulus response to external stimulus regulation of circadian rhythm photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod behavior circadian behavior multicellular organismal process rhythmic behavior locomotory behavior locomotor rhythm protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cellular response to stimulus regulation of signaling signaling regulation of signal transduction signal transduction by p53 class mediator intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of signal transduction by p53 class mediator regulation of cell communication signal transduction negative regulation of biological process 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 transcription by RNA polymerase II 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of biological process positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle cell cycle regulation of cell cycle positive regulation of cellular process proteolysis	cellular anatomical structure membrane intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm membrane-bounded organelle nucleus cellular anatomical structure membrane intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen perinuclear region of cytoplasm
B	Ubiquitin-40S ribosomal protein S27a	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity structural constituent of ribosome cation binding ion binding metal ion binding small molecule binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal small subunit biogenesis catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal small subunit biogenesis catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process 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 biosynthetic process translation gene expression macromolecule biosynthetic process	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 preribosome protein-containing complex ribonucleoprotein complex small-subunit processome cytoplasm ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028889	Ubiquitin specific protease domain	Domain
A	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family
A	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
B	IPR019954	Ubiquitin conserved site	Conserved Site
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR038582	Small ribosomal subunit protein eS31 eukaryotic-type superfamily	Homologous Superfamily
B	IPR002906	Small ribosomal subunit protein eS31	Domain
B	IPR019956	Ubiquitin domain	Domain
B	IPR050158	Ubiquitin and ubiquitin-like	Family
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75604	adenoma atopic eczema Crohn disease hereditary spastic paraplegia malignant glioma pancreatic intraductal papillary-mucinous carcinoma ulcerative colitis adrenal cortex carcinoma atypical teratoid rhabdoid tumor glioblastoma Liver carcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm amyotrophic lateral sclerosis breast cancer adenoma atopic eczema Crohn disease hereditary spastic paraplegia malignant glioma pancreatic intraductal papillary-mucinous carcinoma ulcerative colitis adrenal cortex carcinoma atypical teratoid rhabdoid tumor glioblastoma Liver carcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm amyotrophic lateral sclerosis breast cancer hepatocellular carcinoma malignant colon neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.