2C7N | pdb_00002c7n

Human Rabex-5 residues 1-74 in complex 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)
C	d2c7nc1	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	A20-like zinc finger	RabGEF1 (Rabex-5), ubiquitin-binding domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d2c7ng1	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	A20-like zinc finger	RabGEF1 (Rabex-5), ubiquitin-binding domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d2c7ni1	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	A20-like zinc finger	RabGEF1 (Rabex-5), ubiquitin-binding domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2c7na1	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	A20-like zinc finger	RabGEF1 (Rabex-5), ubiquitin-binding domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2c7nb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	BOVINE (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d2c7nd1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	BOVINE (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
F	d2c7nf1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	BOVINE (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
H	d2c7nh1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	BOVINE (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
J	d2c7nj1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	BOVINE (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
L	d2c7nl1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	BOVINE (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)
C	SCOP2 Family	A20-like zinc finger	8026120	4000506	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8038499	3000068	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8038499	3000068	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8038499	3000068	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8038499	3000068	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8038499	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8038499	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8098440	3000157	SCOP2B (2022-06-29)
L	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)
C	zf-A20	e2c7nC1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-A20	ECOD (v294.1)
E	Hepar_II_III	e2c7nE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (v294.1)
G	zf-A20	e2c7nG1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-A20	ECOD (v294.1)
I	zf-A20	e2c7nI1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-A20	ECOD (v294.1)
K	Hepar_II_III	e2c7nK1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Hepar_II_III	ECOD (v294.1)
A	zf-A20	e2c7nA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: A20-like zinc finger	T: A20-like zinc finger	F: zf-A20	ECOD (v294.1)
B	S4	e2c7nB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
D	S4	e2c7nD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
F	S4	e2c7nF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
H	S4	e2c7nH1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
J	S4	e2c7nJ1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: S4	ECOD (v294.1)
L	S4	e2c7nL1	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)
C	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	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)
G	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)
I	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)
K	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)
A	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	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
H	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
J	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
L	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
A, C, E, G, I A, C, E, G, I, K	PF01754	A20-like zinc finger (zf-A20)	A20-like zinc finger	-	Family
B, D, F, H, J B, D, F, H, J, L	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
A, C, E, G, I A, C, E, G, I, K	RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1	small GTPase binding protein binding binding enzyme binding GTPase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity small GTPase binding protein binding binding enzyme binding GTPase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity DNA binding nucleic acid 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	leukocyte migration immune system process mast cell migration myeloid leukocyte migration cell migration cellular process cell motility interleukin-6 production multicellular organismal process regulation of cellular process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production leukocyte migration immune system process mast cell migration myeloid leukocyte migration cell migration cellular process cell motility interleukin-6 production multicellular organismal process regulation of cellular process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization regulation of immune effector process response to stimulus negative regulation of mast cell cytokine production mast cell cytokine production regulation of immune system process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response regulation of mast cell cytokine production immune response negative regulation of immune effector process immune effector process negative regulation of production of molecular mediator of immune response negative regulation of immune system process regulation of production of molecular mediator of immune response regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response cellular response to stimulus small GTPase-mediated signal transduction signaling negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette signal transduction regulation of signaling Ras protein signal transduction negative regulation of small GTPase mediated signal transduction negative regulation of signal transduction negative regulation of Ras protein signal transduction regulation of cell communication cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein targeting to membrane intracellular transport dendritic transport axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process regulation of localization import into cell regulation of cellular component organization negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization cellular component organization or biogenesis regulation of endocytosis negative regulation of cellular component organization negative regulation of receptor-mediated endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport endocytosis receptor-mediated endocytosis endosomal transport establishment of organelle localization regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte activation myeloid leukocyte mediated immunity leukocyte activation secretion by cell organelle localization leukocyte activation involved in immune response mast cell activation leukocyte mediated immunity mast cell mediated immunity secretion cell activation vacuolar localization export from cell mast cell degranulation myeloid cell activation involved in immune response mast cell activation involved in immune response exocytosis lysosome localization regulation of myeloid leukocyte mediated immunity negative regulation of secretion negative regulation of secretion by cell negative regulation of myeloid leukocyte mediated immunity regulation of secretion regulation of leukocyte mediated immunity negative regulation of regulated secretory pathway negative regulation of leukocyte degranulation regulation of mast cell degranulation regulation of regulated secretory pathway regulation of secretion by cell negative regulation of exocytosis negative regulation of mast cell degranulation regulation of leukocyte degranulation regulation of exocytosis negative regulation of leukocyte mediated immunity response to cytokine negative regulation of Kit signaling pathway cytokine-mediated signaling pathway cell surface receptor protein tyrosine kinase signaling pathway regulation of Kit signaling pathway cellular response to cytokine stimulus enzyme-linked receptor protein signaling pathway cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway cellular response to stem cell factor stimulus response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus Kit signaling pathway negative regulation of cytokine-mediated signaling pathway response to chemical response to stem cell factor immune response-regulating cell surface receptor signaling pathway positive regulation of biological process positive regulation of response to stimulus regulation of Fc receptor mediated stimulatory signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response positive regulation of immune system process immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway regulation of immune response activation of immune response negative regulation of locomotion regulation of cell motility regulation of leukocyte migration negative regulation of leukocyte migration regulation of locomotion regulation of cell migration negative regulation of cell motility negative regulation of cell migration locomotion regulation of leukocyte activation regulation of cell activation negative regulation of cell activation negative regulation of mast cell activation regulation of mast cell activation negative regulation of leukocyte activation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle vesicle endocytic vesicle early endosome endosome endomembrane system endosome membrane membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane recycling endosome synapse presynapse cell junction presynaptic endosome
B, D, F, H, J B, D, F, H, J, L	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
A, C, E, G, I A, C, E, G, I, K	IPR002653	Zinc finger, A20-type	Domain
A, C, E, G, I A, C, E, G, I, K	IPR045046	Vacuolar protein sorting-associated protein 9-like	Family
A, C, E, G, I A, C, E, G, I, K	IPR003123	VPS9 domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR041545	RABX5, catalytic core helical domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR037191	VPS9 domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR019956	Ubiquitin domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR019954	Ubiquitin conserved site	Conserved Site
B, D, F, H, J B, D, F, H, J, L	IPR050158	Ubiquitin and ubiquitin-like	Family
B, D, F, H, J B, D, F, H, J, L	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	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.