Annotations: 2OT3

Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2ot3a_	All alpha proteins	VPS9 domain	VPS9 domain	VPS9 domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ot3b1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab21	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	VPS9 domain	8031274	4002694	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	VPS9 domain	8043652	3001620	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057388	3002022	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	DUF5601	e2ot3A1	A: beta barrels	X: Bromodomain-like	H: RABEX-5 helical domain	T: RABEX-5 helical domain	F: DUF5601	ECOD (v294.2)
A	MRP-L46	e2ot3A2	A: beta barrels	X: SH3	H: Nudix	T: Nudix	F: MRP-L46	ECOD (v294.2)
B	Ras	e2ot3B1	A: beta barrels	X: HTH	H: HTH	T: winged helix domain	F: Ras	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.246.120	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
A	1.20.1050.80	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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
B	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

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 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	Ras-related protein Rab-21	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular localization anterograde axonal transport transport intracellular transport axonal transport establishment of localization localization axo-dendritic transport establishment of localization in cell microtubule-based transport regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular localization anterograde axonal transport transport intracellular transport axonal transport establishment of localization localization axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction axon extension multicellular organismal process regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization neuron projection development multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process nervous system development developmental growth involved in morphogenesis generation of neurons regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension cellular component organization neurogenesis regulation of extent of cell growth cellular component organization or biogenesis regulation of cell size neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of anatomical structure size establishment of protein localization protein transport macromolecule localization intracellular protein localization intracellular protein transport regulation of localization import into cell positive regulation of cellular component organization positive regulation of biological process vesicle-mediated transport positive regulation of endocytosis positive regulation of receptor-mediated endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport positive regulation of transport endocytosis receptor-mediated endocytosis secretion export from cell regulation of secretion regulation of secretion by cell secretion by cell exocytosis regulation of exocytosis positive regulation of early endosome to late endosome transport intercellular transport positive regulation of intracellular transport regulation of intracellular transport endosomal transport vesicle-mediated transport between endosomal compartments regulation of early endosome to late endosome transport early endosome to late endosome transport regulation of cellular localization positive regulation of nervous system development regulation of cell differentiation regulation of neurogenesis regulation of cell morphogenesis regulation of cell development positive regulation of developmental process regulation of dendrite morphogenesis positive regulation of cell projection organization regulation of cell projection organization positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process regulation of neuron projection development regulation of nervous system development positive regulation of cell differentiation dendrite development positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of dendrite morphogenesis dendrite morphogenesis regulation of plasma membrane bounded cell projection organization	cellular anatomical structure endomembrane system anchoring junction cell junction focal adhesion cell-substrate junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cellular anatomical structure endomembrane system anchoring junction cell junction focal adhesion cell-substrate junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol Golgi cisterna membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment membrane Golgi cisterna intracellular membrane-bounded organelle intracellular organelle Golgi stack organelle membrane vesicle membrane cell division site cell periphery cleavage furrow plasma membrane plasma membrane region endosome membrane cytoplasmic side of membrane early endosome intracellular vesicle early endosome membrane cytoplasmic side of endosome membrane bounding membrane of organelle cytoplasmic vesicle cytoplasmic side of early endosome membrane endosome side of membrane cytoplasmic vesicle membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane trans-Golgi network Golgi membrane synapse cytoplasmic side of plasma membrane neuron projection cytoplasm axon cell projection axon cytoplasm neuron projection plasma membrane bounded cell projection

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	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR005225	Small GTP-binding domain	Domain
B	IPR001806	Small GTPase	Family
B	IPR041833	Rab21	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	: Q9UL25	obesity disorder cleft lip large cell medulloblastoma ovarian cancer dermatomyositis lung cancer plasma cell myeloma hereditary spastic paraplegia tuberculosis

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