Annotations: 4I6N

Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4i6nd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4i6nb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4i6nc1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	Trichina worm (Trichinella spiralis ) [TaxId: 6334 ],	SCOPe (2.08)
C	d4i6nc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Trichina worm (Trichinella spiralis ) [TaxId: 6334 ],	SCOPe (2.08)
A	d4i6na1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	Trichina worm (Trichinella spiralis ) [TaxId: 6334 ],	SCOPe (2.08)
A	d4i6na2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Trichina worm (Trichinella spiralis ) [TaxId: 6334 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ubiquitin-like	8097772	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8097772	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)
D	Peptidase_M10	e4i6nD1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Peptidase_M10	ECOD (v295.2)
B	Avidin	e4i6nB1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Avidin	ECOD (v295.2)
C	SH3_1	e4i6nC1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: SH3_1	ECOD (v295.2)
A	Avidin	e4i6nA1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: Avidin	ECOD (v295.2)

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)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	CATH (4.3.0)
A	3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
B, D	Ubiquitin	-	-	membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane cytoplasm organelle membrane nucleus
A, C	Ubiquitin carboxyl-hydrolase	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	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein deubiquitination protein modification by small protein removal macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein deubiquitination protein modification by small protein removal macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation or removal	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR019956	Ubiquitin domain	Domain
B, D	IPR019954	Ubiquitin conserved site	Conserved Site
B, D	IPR050158	Ubiquitin and ubiquitin-like	Family
B, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D	IPR000626	Ubiquitin-like domain	Domain
A, C	IPR041507	Peptidase C12, C-terminal domain	Domain
A, C	IPR036959	Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily	Homologous Superfamily
A, C	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, C	IPR017390	Ubiquitinyl hydrolase, UCH37 type	Family
A, C	IPR001578	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	Domain

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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.