6S6D | pdb_00006s6d

Crystal structure of RagA-Q66L-GTP/RagC-S75N-GDP GTPase heterodimer complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	Ras-like P-loop GTPases	8093371	3002022	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Roadblock/LC7 domain-like	8093374	3001810	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ras-like P-loop GTPases	8093372	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8093372	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Roadblock/LC7 domain-like	8093374	3001810	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)
D	PSII	e6s6dD1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: PSII	ECOD (develop294)
B [auth C]	Lipocalin	e6s6dC1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Lipocalin	ECOD (develop294)
C [auth B]	PSII	e6s6dB1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: PSII	ECOD (develop294)
A	Lipocalin	e6s6dA1	A: alpha bundles	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Lipocalin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C [auth B]	3.30.450.190	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	3.30.450.190	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D	PF04670	Gtr1/RagA G protein conserved region (Gtr1_RagA)	Gtr1/RagA G protein conserved region	GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is ...	GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4].	Domain
A, C [auth B]	PF04670	Gtr1/RagA G protein conserved region (Gtr1_RagA)	Gtr1/RagA G protein conserved region	GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is ...	GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D	Ras-related GTP-binding protein C	protein heterodimerization activity protein binding binding protein dimerization activity 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 protein heterodimerization activity protein binding binding protein dimerization activity 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 enzyme binding GTPase binding enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity cation binding magnesium ion binding metal ion binding GDP binding protein-membrane adaptor activity 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	response to acid chemical response to stimulus response to chemical response to amino acid cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular process TOR signaling regulation of biological process regulation of signaling regulation of cellular process regulation of TOR signaling signaling response to acid chemical response to stimulus response to chemical response to amino acid cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular process TOR signaling regulation of biological process regulation of signaling regulation of cellular process regulation of TOR signaling signaling biological regulation regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication regulation of TORC1 signaling signal transduction TORC1 signaling apoptotic process cell death programmed cell death RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process positive regulation of TORC1 signaling positive regulation of response to stimulus positive regulation of TOR signaling positive regulation of cellular process positive regulation of intracellular signal transduction positive regulation of signaling cellular response to stress response to stress response to starvation cellular response to starvation RNA splicing RNA processing cellular response to acid chemical cellular response to amino acid stimulus cellular response to chemical stimulus protein localization to lysosome localization protein localization to organelle macromolecule localization protein localization to vacuole intracellular protein localization cellular localization localization within membrane protein localization to membrane negative regulation of catabolic process catabolic process negative regulation of metabolic process autophagy negative regulation of biological process regulation of catabolic process regulation of autophagy negative regulation of autophagy negative regulation of cellular process process utilizing autophagic mechanism regulation of metabolic process cellular response to amino acid starvation response to amino acid starvation small GTPase-mediated signal transduction intracellular signaling cassette	GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen lytic vacuole vacuole lysosome catalytic complex GTPase complex Gtr1-Gtr2 GTPase complex vacuolar membrane membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane
A, C [auth B]	Ras-related GTP-binding protein A	phosphoprotein binding protein binding binding protein heterodimerization activity protein dimerization activity 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 phosphoprotein binding protein binding binding protein heterodimerization activity protein dimerization activity 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 protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme 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	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling apoptotic process cell death programmed cell death positive regulation of TORC1 signaling regulation of TORC1 signaling TORC1 signaling cellular response to stress response to stress response to starvation cellular response to starvation cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to chemical response to amino acid protein localization to lysosome localization protein localization to organelle macromolecule localization protein localization to vacuole intracellular protein localization cellular localization localization within membrane protein localization to membrane negative regulation of catabolic process catabolic process negative regulation of metabolic process autophagy negative regulation of biological process regulation of catabolic process regulation of autophagy negative regulation of autophagy negative regulation of cellular process metabolic process process utilizing autophagic mechanism regulation of metabolic process cell surface receptor signaling pathway response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor cellular response to amino acid starvation response to amino acid starvation chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis	GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle GTPase activator complex protein-containing complex FNIP-folliculin RagC/D GAP enzyme activator complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen lytic vacuole vacuole lysosome catalytic complex GTPase complex Gtr1-Gtr2 GTPase complex vacuolar membrane membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR006762	Gtr1/RagA G protein	Family
B [auth C], D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth C], D	IPR039400	RagC/D	Family
A, C [auth B]	IPR039397	RagA/B	Family
A, C [auth B]	IPR006762	Gtr1/RagA G protein	Family
A, C [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], D	Pharos: Q9HB90	follicular lymphoma Lymphoma, Follicular, Grade 3 osteosarcoma
A, C [auth B]	Pharos: Q7L523	large cell medulloblastoma prostate carcinoma ovarian cancer skin basal cell carcinoma pancreatic ductal adenocarcinoma

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.