3CPJ | pdb_00003cpj

Crystal structure of Ypt31 in complex with yeast Rab-GDI

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)
A [auth G]	d3cpjg1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A [auth G]	d3cpjg2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A [auth G]	d3cpjg3	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Ras-like monodomain GTPases	8057509	4004043	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ras-like P-loop GTPases	8057510	3002022	SCOP2 (2022-06-29)
A [auth G]	SCOP2B Superfamily	Flavoreductase-like	8001400	3000055	SCOP2B (2022-06-29)
A [auth G]	SCOP2B Superfamily	Flavoreductase-like	8001400	3000055	SCOP2B (2022-06-29)
A [auth G]	SCOP2B Superfamily	GDI isoprenoid-binding domain-like	8091667	3002533	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)
B	zf-C3HC4_3	e3cpjB1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: zf-C3HC4_3	ECOD (develop294)
A [auth G]	Internalin_N	e3cpjG1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Internalin_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth G]	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A [auth G]	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
A [auth G]	1.10.405.10	Mainly Alpha	Orthogonal Bundle	Guanine Nucleotide Dissociation Inhibitor	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
B	GTP-binding protein YPT31/YPT8	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 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	early endosome to Golgi transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process Golgi vesicle transport catabolic process early endosome to Golgi transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process Golgi vesicle transport catabolic process autophagy metabolic process process utilizing autophagic mechanism establishment of protein localization protein transport macromolecule localization intracellular protein localization secretion by cell exocytosis secretion export from cell	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network endosome membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network endosome intracellular vesicle cytoplasmic vesicle vesicle Golgi membrane membrane bounding membrane of organelle organelle membrane recycling endosome cytosol mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane
A [auth G]	Rab GDP-dissociation inhibitor	GTPase regulator activity enzyme regulator activity GDP-dissociation inhibitor activity nucleoside-triphosphatase regulator activity Rab GDP-dissociation inhibitor activity molecular function regulator activity enzyme activator activity GTPase activator activity molecular function activator activity	localization transport cellular process establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication localization transport cellular process establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette signal transduction establishment of protein localization protein transport macromolecule localization intracellular protein localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR005225	Small GTP-binding domain	Domain
B	IPR001806	Small GTPase	Family
B	IPR050209	Membrane trafficking Rab GTPases	Family
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth G]	IPR000806	Rab GDI protein	Family
A [auth G]	IPR018203	GDP dissociation inhibitor	Family
A [auth G]	IPR036188	FAD/NAD(P)-binding domain superfamily	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.