1VDL | pdb_00001vdl

Solution Structure of RSGI RUH-013, a UBA domain in Mouse cDNA

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)
A	d1vdla1	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	Ubiquitin carboxyl-terminal hydrolase 25	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1vdla3	Artifacts	Tags	Tags	Tags	C-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1vdla2	Artifacts	Tags	Tags	Tags	N-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	UBA domain	8028915	4000749	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UBA-like	8041294	3001235	SCOP2 (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	UBA_4	e1vdlA1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UBA_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22566	UBA-like domain (UBA_8)	UBA-like domain	This entry represents a UBA-like domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin carboxyl-terminal hydrolase 25	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	nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process mRNA metabolic process nucleic acid metabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process mRNA metabolic process nucleic acid metabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein metabolic process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication stress-activated protein kinase signaling cascade cellular response to stress response to stress signal transduction immune response immune system 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 response to oxidative stress cell surface receptor signaling pathway cellular response to interleukin-17 response to interleukin-17 response to cytokine cytokine-mediated signaling pathway response to peptide interleukin-17-mediated signaling pathway response to chemical cellular response to cytokine stimulus	protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex 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
A	IPR028889	Ubiquitin specific protease domain	Domain
A	IPR054108	Ubiquitin carboxyl-terminal hydrolase 25/28, UIM	Conserved Site
A	IPR054109	UBA-like domain	Domain
A	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
A	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR003903	Ubiquitin interacting motif	Conserved Site
A	IPR009060	UBA-like superfamily	Homologous Superfamily

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.