2Q3F

X-ray crystal structure of putative human Ras-related GTP binding D in complex with GMPPNP

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)
A	SCOP2 Family	Gtr1/RagA G domain-like	8046296	4005007	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8093364	3002022	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8093364	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	Gtr1_RagA_N	e2q3fA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gtr1_RagA_N	ECOD (1.6)
B	Gtr1_RagA_N	e2q3fB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gtr1_RagA_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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 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
A, B	Ras-related GTP-binding protein D	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 organic cyclic compound binding purine nucleotide 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 organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding enzyme binding GTPase binding GDP binding molecular 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	protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus 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 response to nutrient levels cellular response to leucine starvation cellular response to amino acid starvation cellular response to starvation cellular response to nutrient levels cellular response to stress response to stress response to amino acid starvation response to starvation positive regulation of TORC1 signaling regulation of TORC1 signaling TORC1 signaling 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 negative regulation of cellular catabolic process negative regulation of catabolic process catabolic process cellular metabolic process negative regulation of metabolic process autophagy negative regulation of biological process regulation of cellular metabolic process regulation of catabolic process regulation of autophagy negative regulation of cellular metabolic process cellular catabolic process negative regulation of autophagy regulation of cellular catabolic process negative regulation of cellular process metabolic process process utilizing autophagic mechanism regulation of metabolic process cellular response to nitrogen compound response to organonitrogen compound response to endogenous stimulus response to oxygen-containing compound response to nitrogen compound cellular response to L-leucine cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to organonitrogen compound response to L-leucine	intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle intracellular membrane-bounded organelle intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lytic vacuole vacuole lysosome protein-containing complex 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
A, B	IPR006762	Gtr1/RagA G protein	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR039400	RagC/D	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9NQL2	Barrett esophagus cystic fibrosis invasive ductal breast carcinoma malignant colon neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis breast cancer ductal breast carcinoma in situ large cell medulloblastoma malignant mesothelioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis cutaneous lupus erythematosus Barrett esophagus cystic fibrosis invasive ductal breast carcinoma malignant colon neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis breast cancer ductal breast carcinoma in situ large cell medulloblastoma malignant mesothelioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis cutaneous lupus erythematosus esophageal adenocarcinoma lung cancer medulloblastoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma

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 R01GM133198.