2FIF

Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin

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	d2fifa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d2fifc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E	d2fife_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d2fifb_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	A20-like zinc finger	RabGEF1 (Rabex-5), ubiquitin-binding domain	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d2fifd_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	A20-like zinc finger	RabGEF1 (Rabex-5), ubiquitin-binding domain	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
F	d2fiff_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	A20-like zinc finger	RabGEF1 (Rabex-5), ubiquitin-binding domain	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
B	SCOP2 Family	A20-like zinc finger	8028582	4000506	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040961	3000068	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040961	3000068	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040961	3000068	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)
A	ubiquitin_1	e2fifA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C	ubiquitin_1	e2fifC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
E	ubiquitin_1	e2fifE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	zf-A20	e2fifB1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: A20-like zinc finger (From Topology)	T: A20-like zinc finger	F: zf-A20	ECOD (1.6)
D	zf-A20	e2fifD1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: A20-like zinc finger (From Topology)	T: A20-like zinc finger	F: zf-A20	ECOD (1.6)
F	zf-A20	e2fifF1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: A20-like zinc finger (From Topology)	T: A20-like zinc finger	F: zf-A20	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	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)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	1.20.5.4770	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D	1.20.5.4770	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
F	1.20.5.4770	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, 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
B, D, F	PF01754	A20-like zinc finger (zf-A20)	A20-like zinc finger	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification post-translational protein modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic 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 mitochondrial membrane mitochondrion membrane organelle outer membrane cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane cytoplasm organelle membrane nucleus
B, D, F	Rab5 GDP/GTP exchange factor	DNA binding binding organic cyclic compound binding nucleic acid binding small GTPase binding protein binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding DNA binding binding organic cyclic compound binding nucleic acid binding small GTPase binding protein binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	localization import into cell transport cellular process endocytosis establishment of localization vesicle-mediated transport protein localization establishment of protein localization cellular localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome cytosol endocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR019956	Ubiquitin domain	Domain
A, C, E	IPR019954	Ubiquitin conserved site	Conserved Site
A, C, E	IPR050158	Ubiquitin and ubiquitin-like	Family
A, C, E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C, E	IPR000626	Ubiquitin-like domain	Domain
B, D, F	IPR041545	RABX5, catalytic core helical domain	Domain
B, D, F	IPR002653	Zinc finger, A20-type	Domain
B, D, F	IPR037191	VPS9 domain superfamily	Homologous Superfamily
B, D, F	IPR045046	Vacuolar protein sorting-associated protein 9-like	Family
B, D, F	IPR003123	VPS9 domain	Domain

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.