2FIF | pdb_00002fif

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)
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)
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)
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)
E	d2fife_	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)
A	d2fifa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(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)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040961	3000068	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040961	3000068	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)
E	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8098440	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)
F	zf-A20	e2fifF1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-A20	ECOD (v294.1)
D	zf-A20	e2fifD1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-A20	ECOD (v294.1)
B	zf-A20	e2fifB1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-A20	ECOD (v294.1)
E	S4	e2fifE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
C	S4	e2fifC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
A	S4	e2fifA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
E	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)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	Rab5 GDP/GTP exchange factor	DNA binding 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 DNA binding 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 establishment of protein localization protein transport macromolecule localization intracellular protein localization	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome cytosol endocytic vesicle
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 modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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

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.