Structure of PDB 4arz Chain B Binding Site BS01

Receptor Information
>4arz Chain B (length=304) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATDSKAMVLLMGVRRCGKSSICKVVFHNMQPLDTLYLESTSNPSLEHFST
LIDLAVMELPGQLNYFEPSYDSERLFKSVGALVYVIDSQDEYINAITNLA
MIIEYAYKVNPSINIEVLIHKVDGLSEDFKVDAQRDIMQRTGEELLELGL
DGVQVSFYLTSIFDHSIYEAFSRIVQKLIPELSFLENMLDNLIQHSKIEK
AFLFDVNSKIYVSTDSNPVDIQMYEVCSEFIDVTIDLFDLYKAPRNELQN
VSQLANGVIIYLRQMIRGLALVAIIRPNGTDMESCLTVADYNIDIFKKGL
EDIW
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4arz Chain B Residue 400 [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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PDB4arz Crystal Structure of the Gtr1Pgtp-Gtr2Pgdp Complex Reveals Large Structural Rearrangements Triggered by GTP-to-Gdp Conversion
Resolution3.1 Å
Binding residue
(original residue number in PDB)		R19 C20 G21 K22 S23 S24 H124 K125 D127 S165 I166 F167
Binding residue
(residue number reindexed from 1)		R15 C16 G17 K18 S19 S20 H120 K121 D123 S161 I162 F163
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
Biological Process
GO:0006995 cellular response to nitrogen starvation
GO:0009267 cellular response to starvation
GO:0010507 negative regulation of autophagy
GO:0016237 microautophagy
GO:0032008 positive regulation of TOR signaling
GO:0032456 endocytic recycling
GO:0034599 cellular response to oxidative stress
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0071230 cellular response to amino acid stimulus
GO:1903778 protein localization to vacuolar membrane
GO:1904263 positive regulation of TORC1 signaling
Cellular Component
GO:0000329 fungal-type vacuole membrane
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005770 late endosome
GO:0005773 vacuole
GO:0005774 vacuolar membrane
GO:0016020 membrane
GO:0031902 late endosome membrane
GO:0045121 membrane raft
GO:0071986 Ragulator complex
GO:1990131 Gtr1-Gtr2 GTPase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4arz, PDBe:4arz, PDBj:4arz
PDBsum4arz
PubMed22807443
UniProtP53290|RAGCD_YEAST GTP-binding protein GTR2 (Gene Name=GTR2)

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