3CPH

Crystal structure of Sec4 in complex with 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]	d3cphg1	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]	d3cphg2	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]	d3cphg3	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)
C [auth H]	d3cphh1	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)
C [auth H]	d3cphh2	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)
C [auth H]	d3cphh3	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)
B [auth A]	d3cpha_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	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)
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)
C [auth H]	SCOP2B Superfamily	GDI isoprenoid-binding domain-like	8091667	3002533	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Flavoreductase-like	8001400	3000055	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Flavoreductase-like	8001400	3000055	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Ras-like P-loop GTPases	8057408	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 [auth G]	PF00996	e3cphG1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: PF00996	ECOD (1.6)
A [auth G]	PF00996	e3cphG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF00996	ECOD (1.6)
C [auth H]	PF00996	e3cphH1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: PF00996	ECOD (1.6)
C [auth H]	PF00996	e3cphH2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF00996	ECOD (1.6)
B [auth A]	PF00071	e3cphA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
C [auth H]	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C [auth H]	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
C [auth H]	1.10.405.10	Mainly Alpha	Orthogonal Bundle	Guanine Nucleotide Dissociation Inhibitor	domain 1	CATH (4.3.0)
B [auth A]	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 [auth G], C [auth H]	PF00996	GDP dissociation inhibitor (GDI)	GDP dissociation inhibitor	-	Family
B [auth A]	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 [auth G], C [auth H]	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 protein localization establishment of protein localization cellular localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization	intracellular anatomical structure cytoplasm cellular anatomical entity
B [auth A]	Ras-related protein SEC4	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 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 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	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 cellular process Golgi vesicle transport cellular catabolic process catabolic process cellular metabolic process 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 cellular process Golgi vesicle transport cellular catabolic process catabolic process cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism membrane organization membrane fusion organelle membrane fusion vesicle organization cellular component organization organelle fusion organelle organization cellular component organization or biogenesis vesicle fusion secretion export from cell membrane docking organelle localization by membrane tethering secretion by cell exocytosis organelle localization vesicle docking exocytic process vesicle docking involved in exocytosis protein localization protein localization to cell periphery protein localization to plasma membrane cellular macromolecule localization macromolecule localization protein localization to membrane cytokinetic process cell cycle cytokinesis cell division membrane addition at site of cytokinesis cell cycle process establishment of protein localization nitrogen compound transport organic substance transport establishment of protein localization to extracellular region protein secretion protein localization to extracellular region protein transport regulation of localization regulation of biological process regulation of cellular process regulation of transport biological regulation regulation of vesicle-mediated transport regulation of secretion regulation of secretion by cell regulation of exocytosis sexual reproduction cellular developmental process cellular component assembly involved in morphogenesis reproductive process cell development developmental process involved in reproduction meiotic cell cycle process cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly sexual sporulation cell differentiation anatomical structure development developmental process sexual sporulation resulting in formation of a cellular spore reproductive process in single-celled organism meiotic cell cycle sporulation resulting in formation of a cellular spore anatomical structure morphogenesis ascospore formation ascospore-type prospore assembly anatomical structure formation involved in morphogenesis sporulation	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle incipient cellular bud site site of polarized growth vesicle cell projection mating projection cell tip membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle incipient cellular bud site site of polarized growth vesicle cell projection mating projection cell tip mating projection tip cell pole plasma membrane bounded cell projection cell periphery plasma membrane membrane transport vesicle intracellular vesicle endomembrane system cytoplasmic vesicle endosome mitochondrial membrane organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane cellular bud neck cellular bud transport vesicle membrane cytoplasmic vesicle membrane vesicle membrane endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], C [auth H]	IPR000806	Rab GDI protein	Family
A [auth G], C [auth H]	IPR018203	GDP dissociation inhibitor	Family
A [auth G], C [auth H]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth A]	IPR001806	Small GTPase	Family
B [auth A]	IPR005225	Small GTP-binding protein domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.