4N3Z

Crystal structure of Rabex-5delta and Rabaptin-5C21 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4n3zb_	Coiled coil proteins	Parallel coiled-coil	G protein-binding domain	Rabaptin-5	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4n3zc_	Coiled coil proteins	Parallel coiled-coil	G protein-binding domain	Rabaptin-5	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	VPS9_1	e4n3zA1	A: alpha bundles	X: Bromodomain-like	H: RABEX-5 helical domain (From Topology)	T: RABEX-5 helical domain	F: VPS9_1	ECOD (1.6)
A	KOG2319_like_2nd	e4n3zA2	A: alpha complex topology	X: VPS9 domain (From Topology)	H: VPS9 domain (From Topology)	T: VPS9 domain	F: KOG2319_like_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1050.80	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18151	Domain of unknown function (DUF5601) (DUF5601)	Domain of unknown function (DUF5601)	This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature ...	This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature [1].	Domain
A	PF02204	Vacuolar sorting protein 9 (VPS9) domain (VPS9)	Vacuolar sorting protein 9 (VPS9) domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Rab5 GDP/GTP exchange factor	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 organic cyclic compound 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 cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of interleukin-6 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 cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic 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 cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular 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 protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization regulation of immune effector process response to stimulus negative regulation of mast cell cytokine production regulation of immune system process negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response immune response negative regulation of immune effector process immune effector process negative regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response mast cell cytokine production myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response regulation of mast cell cytokine production negative regulation of immune system process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process primary metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation 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 establishment of protein localization to membrane protein targeting localization within membrane protein localization to 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 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 membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle 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
B, C	Rab GTPase-binding effector protein 1	protein binding binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity GTPase regulator activity protein binding binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity nucleoside-triphosphatase regulator activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis Golgi to plasma membrane transport cellular localization post-Golgi vesicle-mediated transport transport localization within membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis Golgi to plasma membrane transport cellular localization post-Golgi vesicle-mediated transport transport localization within membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization Golgi vesicle transport import into cell endocytosis protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization apoptotic process cell death programmed cell death protein localization to cell periphery protein localization to cilium protein localization to membrane protein localization to ciliary membrane protein localization to organelle	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 endosome membrane 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 endosome membrane membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane recycling endosome endocytic vesicle protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002653	Zinc finger, A20-type	Domain
A	IPR045046	Vacuolar protein sorting-associated protein 9-like	Family
A	IPR003123	VPS9 domain	Domain
A	IPR041545	RABX5, catalytic core helical domain	Domain
A	IPR037191	VPS9 domain superfamily	Homologous Superfamily
B, C	IPR003914	Rabaptin	Family
B, C	IPR015390	Rabaptin, GTPase-Rab5 binding domain	Domain
B, C	IPR018514	Rabaptin coiled-coil domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, C	Pharos: Q15276	rheumatoid arthritis breast cancer hereditary spastic paraplegia ovarian cancer psoriasis Gaucher disease malignant glioma pancreatic ductal adenocarcinoma glioblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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 R01GM133198.