5O74 | pdb_00005o74

Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP

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)
F	d5o74f_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d5o74l_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d5o74j_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5o74h_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5o74d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5o74b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	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)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	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)
F	Terminase_6N	e5o74F1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
L	Terminase_6N	e5o74L1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
J	Terminase_6N	e5o74J1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
H	Terminase_6N	e5o74H1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
D	Terminase_6N	e5o74D1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
B	Terminase_6N	e5o74B1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
C	Terminase_6N	e5o74C1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
I	Terminase_6N	e5o74I1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
K	Terminase_6N	e5o74K1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
G	Terminase_6N	e5o74G1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
E	Terminase_6N	e5o74E1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)
A	Terminase_6N	e5o74A1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
L	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
J	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H	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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
I	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
K	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
G	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
E	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
A	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	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, D, F, H, J B, D, F, H, J, L	Ras-related protein Rab-1B	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 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	virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological process regulation of cellular process positive regulation of glycoprotein metabolic process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process carbohydrate derivative metabolic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process regulation of primary metabolic process regulation of glycoprotein metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process regulation of cellular component organization regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly localization cellular localization transport establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport establishment of protein localization protein transport macromolecule localization intracellular protein localization intracellular protein transport Golgi organization endomembrane system organization	cellular anatomical structure endomembrane system extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure endomembrane system extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol phagophore assembly site membrane membrane phagophore assembly site transport vesicle intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane Golgi apparatus Golgi membrane bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment perinuclear region of cytoplasm
A, C, E, G, I A, C, E, G, I, K	Multifunctional virulence effector protein DrrA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding small GTPase binding protein binding enzyme binding GTPase binding protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol binding adenylyltransferase activity AMPylase activity	regulation of molecular function regulation of catalytic activity regulation of hydrolase activity biological regulation regulation of GTPase activity protein nucleotidylation protein adenylylation macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of molecular function regulation of catalytic activity regulation of hydrolase activity biological regulation regulation of GTPase activity protein nucleotidylation protein adenylylation macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein guanylylation	cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR005225	Small GTP-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR001806	Small GTPase	Family
B, D, F, H, J B, D, F, H, J, L	IPR050227	Ras-related protein Rab	Family
B, D, F, H, J B, D, F, H, J, L	IPR057289	Rab1/Ypt1	Family
A, C, E, G, I A, C, E, G, I, K	IPR048718	SidM, Rab1-activation domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR038346	DrrA, PI4P binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR028057	DrrA phosphatidylinositol 4-phosphate binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR048717	SidM, N-terminal domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR033784	SidM, Rab1-activation domain, Legionella pneumophila	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L	Pharos: Q9H0U4	astrocytic tumor coronary artery disease ovarian carcinoma bipolar disorder gout prostate carcinoma breast carcinoma myocardial ischemia

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.