2EFD

Ara7/AtVps9a

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)
B	d2efdb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d2efdd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057484	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057484	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)
C	KOG2319_like_1st	e2efdC2	A: alpha bundles	X: Bromodomain-like	H: RABEX-5 helical domain (From Topology)	T: RABEX-5 helical domain	F: KOG2319_like_1st	ECOD (1.6)
C	VPS9	e2efdC1	A: alpha complex topology	X: VPS9 domain (From Topology)	H: VPS9 domain (From Topology)	T: VPS9 domain	F: VPS9	ECOD (1.6)
A	KOG2319_like_1st	e2efdA2	A: alpha bundles	X: Bromodomain-like	H: RABEX-5 helical domain (From Topology)	T: RABEX-5 helical domain	F: KOG2319_like_1st	ECOD (1.6)
A	VPS9	e2efdA1	A: alpha complex topology	X: VPS9 domain (From Topology)	H: VPS9 domain (From Topology)	T: VPS9 domain	F: VPS9	ECOD (1.6)
B	Ras	e2efdB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
D	Ras	e2efdD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.246.120	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
C	1.20.1050.80	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (4.3.0)
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)
D	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, C	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, C	PF02204	Vacuolar sorting protein 9 (VPS9) domain (VPS9)	Vacuolar sorting protein 9 (VPS9) domain	-	Family
B, D	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, motil ...	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, C	Similarity to vacuolar protein sorting-associated protein VPS9	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding guanyl-nucleotide exchange factor activity	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport developmental process multicellular organismal process reproductive system development reproductive process localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport developmental process multicellular organismal process reproductive system development reproductive process embryo development developmental process involved in reproduction multicellular organism development fruit development embryo development ending in seed dormancy seed development anatomical structure development reproductive structure development post-embryonic development system development plant organ development post-embryonic root development post-embryonic plant organ development root development root system development cytokinesis cell plate assembly cellular component biogenesis cellular component organization cellular component assembly cytokinesis by cell plate formation cellular component organization or biogenesis cell division cell cycle cell cycle process cell wall biogenesis cell wall organization or biogenesis	-
B, D	Small GTP-binding protein-like	binding small molecule binding molecular sequestering activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding binding small molecule binding molecular sequestering activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport late endosome to vacuole transport vacuolar transport vesicle-mediated transport cellular component organization organelle organization vacuole organization cellular component organization or biogenesis	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 endosome membrane 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 endosome membrane membrane multivesicular body membrane late endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane late endosome organelle membrane multivesicular body early endosome membrane cell periphery plasma membrane endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR041545	RABX5, catalytic core helical domain	Domain
A, C	IPR037191	VPS9 domain superfamily	Homologous Superfamily
A, C	IPR045046	Vacuolar protein sorting-associated protein 9-like	Family
A, C	IPR003123	VPS9 domain	Domain
B, D	IPR005225	Small GTP-binding domain	Domain
B, D	IPR001806	Small GTPase	Family
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.