2G45

Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) 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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2g45a_	Small proteins	RING/U-box	RING/U-box	Zf-UBP	Ubiquitin carboxyl-terminal hydrolase 5, UBP5	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d2g45d_	Small proteins	RING/U-box	RING/U-box	Zf-UBP	Ubiquitin carboxyl-terminal hydrolase 5, UBP5	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2g45b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d2g45e_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Zf-UBP	8020510	4002865	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RING/U-box like	8032890	3000160	SCOP2 (2022-06-29)
C [auth D]	SCOP2B Superfamily	RING/U-box like	8032890	3000160	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Ubiquitin-like	8043829	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	zf-UBP	e2g45A1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-UBP	ECOD (1.6)
C [auth D]	zf-UBP	e2g45D1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-UBP	ECOD (1.6)
B	ubiquitin_1	e2g45B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D [auth E]	ubiquitin_1	e2g45E1	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	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C [auth D]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D [auth E]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF02148	Zn-finger in ubiquitin-hydrolases and other protein (zf-UBP)	Zn-finger in ubiquitin-hydrolases and other protein	-	Domain
B, D [auth E]	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, C [auth D]	Ubiquitin carboxyl-terminal hydrolase 5	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type endopeptidase activity endopeptidase activity protein binding binding ubiquitin binding ubiquitin-like protein binding cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type endopeptidase activity endopeptidase activity protein binding binding ubiquitin binding ubiquitin-like protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein deubiquitination organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein modification by small protein removal macromolecule modification nitrogen compound metabolic process metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein K48-linked deubiquitination protein modification by small protein conjugation or removal protein deubiquitination organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein modification by small protein removal macromolecule modification nitrogen compound metabolic process metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein K48-linked deubiquitination protein modification by small protein conjugation or removal catabolic process negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process negative regulation of biological process negative regulation of nitrogen compound metabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic 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 macromolecule metabolic process organonitrogen compound catabolic process negative regulation of catabolic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of catabolic process regulation of macromolecule metabolic process protein catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of metabolic process organic substance catabolic process positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process positive regulation of macromolecule metabolic process proteasomal protein catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process positive regulation of nitrogen compound metabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein catabolic process protein ubiquitination protein modification by small protein conjugation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle lytic vacuole vacuole intracellular membrane-bounded organelle lysosome nucleus
B, D [auth E]	Ubiquitin	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis nitrogen compound metabolic process metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis nitrogen compound metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic 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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D]	IPR028889	Ubiquitin specific protease domain	Domain
A, C [auth D]	IPR016652	Ubiquitinyl hydrolase	Family
A, C [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C [auth D]	IPR041432	Ubiquitinyl hydrolase, variant UBP zinc finger	Domain
A, C [auth D]	IPR001607	Zinc finger, UBP-type	Domain
A, C [auth D]	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, C [auth D]	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, C [auth D]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, C [auth D]	IPR009060	UBA-like superfamily	Homologous Superfamily
A, C [auth D]	IPR041812	Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain	Domain
A, C [auth D]	IPR015940	Ubiquitin-associated domain	Domain
B, D [auth E]	IPR019954	Ubiquitin conserved site	Conserved Site
B, D [auth E]	IPR000626	Ubiquitin-like domain	Domain
B, D [auth E]	IPR019956	Ubiquitin domain	Domain
B, D [auth E]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth D]	Pharos: P45974	colorectal cancer large cell medulloblastoma diabetes mellitus drug-induced liver injury
B, D [auth E]	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.