Structure of PDB 6s6d Chain B Binding Site BS01

Receptor Information
>6s6d Chain B (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFL
GNLVLNLWDCGGLDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDM
HYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSR
PLECACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEV
LLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSME
VRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERV
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain6s6d Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6s6d Architecture of human Rag GTPase heterodimers and their complex with mTORC1.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		S16 G17 G19 K20 T21 S22 T36 T42 G64 G65 H127 K128 D130 S163 I164
Binding residue
(residue number reindexed from 1)		S13 G14 G16 K17 T18 S19 T33 T39 G61 G62 H124 K125 D127 S160 I161
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0031625 ubiquitin protein ligase binding
GO:0042803 protein homodimerization activity
GO:0043495 protein-membrane adaptor activity
GO:0046982 protein heterodimerization activity
GO:0051219 phosphoprotein binding
Biological Process
GO:0006915 apoptotic process
GO:0008104 protein localization
GO:0009267 cellular response to starvation
GO:0010507 negative regulation of autophagy
GO:0031669 cellular response to nutrient levels
GO:0032008 positive regulation of TOR signaling
GO:0033209 tumor necrosis factor-mediated signaling pathway
GO:0034198 cellular response to amino acid starvation
GO:0035556 intracellular signal transduction
GO:0042593 glucose homeostasis
GO:0061462 protein localization to lysosome
GO:0071230 cellular response to amino acid stimulus
GO:0072657 protein localization to membrane
GO:1904263 positive regulation of TORC1 signaling
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:1990130 GATOR1 complex
GO:1990131 Gtr1-Gtr2 GTPase complex
GO:1990877 FNIP-folliculin RagC/D GAP

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6s6d, PDBe:6s6d, PDBj:6s6d
PDBsum6s6d
PubMed31601764
UniProtQ7L523|RRAGA_HUMAN Ras-related GTP-binding protein A (Gene Name=RRAGA)

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