1VEK | pdb_00001vek

Solution Structure of RSGI RUH-011, a UBA Domain from Arabidopsis 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	d1veka1	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	Ubiquitin isopeptidase T	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d1veka3	Artifacts	Tags	Tags	Tags	C-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d1veka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	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	8030696	4000749	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UBA-like	8043075	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	e1vekA1	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	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 (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22562	UBA-like domain (UBA_7)	UBA-like domain	This entry represents a UBA domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ubiquitin-specific protease 14, putative	protein binding binding ubiquitin binding ubiquitin-like protein binding linear polyubiquitin binding cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein Met1-linked polyubiquitin deubiquitinase activity hydrolase activity catalytic activity deubiquitinase activity protein binding binding ubiquitin binding ubiquitin-like protein binding linear polyubiquitin binding cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein Met1-linked polyubiquitin deubiquitinase activity hydrolase activity catalytic activity deubiquitinase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	multicellular organismal process plant epidermal cell differentiation cellular developmental process developmental growth plant epidermis development cell development cell growth multicellular organism development root hair cell development cell differentiation anatomical structure development cell maturation root development trichoblast differentiation multicellular organismal process plant epidermal cell differentiation cellular developmental process developmental growth plant epidermis development cell development cell growth multicellular organism development root hair cell development cell differentiation anatomical structure development cell maturation root development trichoblast differentiation system development developmental process root hair elongation plant organ development developmental cell growth root morphogenesis root epidermal cell differentiation growth root hair cell differentiation developmental maturation tissue development developmental growth involved in morphogenesis plant organ morphogenesis anatomical structure morphogenesis trichoblast maturation anatomical structure maturation cellular process root system development leaf morphogenesis shoot system morphogenesis leaf development shoot system development phyllome development reproductive system development reproductive process embryo development developmental process involved in reproduction fruit development embryo development ending in seed dormancy seed development reproductive structure development post-embryonic development regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation biological regulation protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal auxin-activated signaling pathway cellular response to stimulus response to stimulus signaling response to endogenous stimulus hormone-mediated signaling pathway cellular response to auxin stimulus cell communication response to auxin cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical signal transduction cellular response to hormone stimulus proteolysis cellular response to gibberellin stimulus response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to gibberellin cellular response to lipid	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016652	Ubiquitinyl hydrolase	Family
A	IPR041432	Ubiquitinyl hydrolase, variant UBP zinc finger	Domain
A	IPR001607	Zinc finger, UBP-type	Domain
A	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family
A	IPR015940	Ubiquitin-associated domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
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.