3I3T | pdb_00003i3t

Crystal structure of covalent ubiquitin-USP21 complex

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)
H	d3i3th_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth F]	d3i3tf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d3i3td_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d3i3tb_	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 G]	d3i3tg_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d3i3te_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3i3tc_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3i3ta_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	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)
H	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Ubiquitin-like	8066187	3000157	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8067279	3001808	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)
H	Ribosomal_L36	e3i3tH1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
G [auth F]	Ribosomal_L36	e3i3tF1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
F [auth D]	Ribosomal_L36	e3i3tD1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
E [auth B]	Ribosomal_L36	e3i3tB1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
D [auth G]	Ribosomal_L36	e3i3tG1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
C [auth E]	Ribosomal_L36	e3i3tE1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
B [auth C]	Ribosomal_L36	e3i3tC1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)
A	Ribosomal_L36	e3i3tA1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G [auth F]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
F [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E [auth B]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D [auth G]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C [auth E]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B [auth C]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
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
E [auth B], F [auth D], G [auth F], H	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
A, B [auth C], C [auth E], D [auth G]	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth B], F [auth D], G [auth F], H	Ubiquitin	structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic process macromolecule catabolic process protein ubiquitination post-translational protein modification macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic process macromolecule catabolic process protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation response to stimulus response to chemical response to insecticide response to toxic substance	membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery membrane-bounded organelle cellular anatomical structure organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit
A, B [auth C], C [auth E], D [auth G]	Ubiquitin carboxyl-terminal hydrolase 21	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 deNEDDylase activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity 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 deNEDDylase activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process protein deubiquitination 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 proteolysis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth B], F [auth D], G [auth F], H	IPR019954	Ubiquitin conserved site	Conserved Site
E [auth B], F [auth D], G [auth F], H	IPR038587	Large ribosomal subunit protein eL40 superfamily	Homologous Superfamily
E [auth B], F [auth D], G [auth F], H	IPR050158	Ubiquitin and ubiquitin-like	Family
E [auth B], F [auth D], G [auth F], H	IPR000626	Ubiquitin-like domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR019956	Ubiquitin domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR001975	Large ribosomal subunit protein eL40 domain	Domain
E [auth B], F [auth D], G [auth F], H	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, B [auth C], C [auth E], D [auth G]	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B [auth C], C [auth E], D [auth G]	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B [auth C], C [auth E], D [auth G]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth B], F [auth D], G [auth F], H	Pharos: P62987	attention deficit hyperactivity disorder, inattentive type heart disease dental caries lung cancer gastroesophageal reflux disease plasma cell myeloma
A, B [auth C], C [auth E], D [auth G]	Pharos: Q9UK80	allergic rhinitis ovarian cancer lung cancer malignant mesothelioma

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.