4BOS

Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide

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)
C	d4bosc_	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]	d4bose_	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)
C	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)
B	OTU	e4bosB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: OTU	ECOD (1.6)
A	OTU	e4bosA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: OTU	ECOD (1.6)
C	ubiquitin_1	e4bosC1	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	e4bosE1	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)
B	3.90.70.80	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.90.70.80	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	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)
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, B	PF02338	OTU-like cysteine protease (OTU)	OTU-like cysteine protease	-	Family
C, 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
E [auth F]	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, B	UBIQUITIN THIOESTERASE OTU1	K63-linked deubiquitinase activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity K48-linked deubiquitinase activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding K63-linked deubiquitinase activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity K48-linked deubiquitinase activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation 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 protein K27-linked deubiquitination metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cellular catabolic process protein deubiquitination organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein modification by small protein removal macromolecule modification protein K27-linked deubiquitination metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process process utilizing autophagic mechanism protein K11-linked deubiquitination protein K48-linked deubiquitination protein K29-linked deubiquitination protein K33-linked deubiquitination protein localization cellular response to stimulus negative regulation of protein transport regulation of localization establishment of protein localization response to organic substance nitrogen compound transport regulation of cellular process response to stimulus negative regulation of biological process negative regulation of intracellular protein transport negative regulation of transport localization ERAD pathway proteolysis establishment of localization in cell cellular macromolecule localization negative regulation of protein exit from endoplasmic reticulum regulation of intracellular transport response to endoplasmic reticulum stress organonitrogen compound catabolic process regulation of biological process response to organonitrogen compound organic substance transport negative regulation of establishment of protein localization intracellular transport response to nitrogen compound establishment of localization response to chemical regulation of intracellular protein transport intracellular protein transport regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum cellular localization regulation of protein localization transport proteolysis involved in protein catabolic process macromolecule catabolic process regulation of retrograde protein transport, ER to cytosol cellular response to stress response to stress negative regulation of cellular process negative regulation of protein localization negative regulation of intracellular transport endoplasmic reticulum to cytosol transport regulation of transport biological regulation regulation of establishment of protein localization proteasomal protein catabolic process regulation of protein transport protein catabolic process protein transport regulation of cellular localization macromolecule localization retrograde protein transport, ER to cytosol negative regulation of retrograde protein transport, ER to cytosol organic substance catabolic process protein K63-linked deubiquitination cellular response to topologically incorrect protein signaling endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein cell communication cellular response to chemical stimulus response to topologically incorrect protein signal transduction cellular response to organic substance	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
C, D [auth E]	POLYUBIQUITIN-C	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 metabolic process protein metabolic process macromolecule 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 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
E [auth F]	OTUD2	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 metabolic process protein metabolic process macromolecule 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 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, B	IPR013087	Zinc finger C2H2-type	Domain
A, B	IPR003323	OTU domain	Domain
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B	IPR048857	OTU1, Ubl domain	Domain
C, D [auth E]	IPR019954	Ubiquitin conserved site	Conserved Site
C, D [auth E]	IPR000626	Ubiquitin-like domain	Domain
C, D [auth E]	IPR019956	Ubiquitin domain	Domain
C, D [auth E]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
E [auth F]	IPR019954	Ubiquitin conserved site	Conserved Site
E [auth F]	IPR000626	Ubiquitin-like domain	Domain
E [auth F]	IPR019956	Ubiquitin domain	Domain
E [auth F]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q5VVQ6	atopic eczema large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm pneumonia tuberculosis attention deficit hyperactivity disorder, inattentive type lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis vascular disease diabetes mellitus malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous carcinoma atopic eczema large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm pneumonia tuberculosis attention deficit hyperactivity disorder, inattentive type lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis vascular disease diabetes mellitus malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous carcinoma periodontitis spina bifida
C, 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
E [auth F]	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.