1LV0 | pdb_00001lv0

Crystal structure of the Rab effector guanine nucleotide dissociation inhibitor (GDI) in complex with a geranylgeranyl (GG) peptide

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	d1lv0a1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	Guanine nucleotide dissociation inhibitor, GDI	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1lv0a2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GDI-like	Guanine nucleotide dissociation inhibitor, GDI	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1lv0a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GDI-like	8056250	4000126	SCOP2 (2022-06-29)
A	SCOP2 Family	GDI isoprenoid-binding domain-like	8091670	4007752	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoreductase-like	8056251	3000055	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GDI isoprenoid-binding domain-like	8091671	3002533	SCOP2 (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	YceM-like_C	e1lv0A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: YceM-like_C	ECOD (v294.1)
A	NAD_binding_8	e1lv0A2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_8	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
A	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
A	PF00996	GDP dissociation inhibitor (GDI)	GDP dissociation inhibitor	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RAB GDP disossociation inhibitor alpha	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 regulation of localization cellular localization establishment of protein localization regulation of cellular process regulation of protein localization protein targeting negative regulation of biological process regulation of protein targeting to membrane negative regulation of cellular process localization transport cellular process establishment of localization vesicle-mediated transport regulation of localization cellular localization establishment of protein localization regulation of cellular process regulation of protein localization protein targeting negative regulation of biological process regulation of protein targeting to membrane negative regulation of cellular process intracellular protein localization regulation of biological process establishment of protein localization to membrane biological regulation regulation of establishment of protein localization negative regulation of protein targeting to membrane negative regulation of establishment of protein localization localization within membrane protein targeting to membrane regulation of cellular localization regulation of protein targeting macromolecule localization multicellular organismal process axonogenesis cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process negative regulation of cellular component organization regulation of cell projection organization nervous system development generation of neurons negative regulation of axonogenesis negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of axonogenesis negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization negative regulation of developmental process axon development negative regulation of neuron projection development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis negative regulation of cell development neuron development regulation of plasma membrane bounded cell projection organization cellular response to stimulus small GTPase-mediated signal transduction response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction protein transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000806	Rab GDI protein	Family
A	IPR018203	GDP dissociation inhibitor	Family
A	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.

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