Structure of PDB 1yr7 Chain A Binding Site BS01

Receptor Information
>1yr7 Chain A (length=243) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLDTGVKELPYEPSID
VREFVTVEEIMREGYGPNGAIVESYDRLMEKFNEYLNKILRLEKENDYVL
IDTPGQMETFLFHEFGVRLMENLPYPLVVYISDPEILKKPNDYCFVRFFA
LLIDLRLGATTIPALNKVDLLSEEEKERHRKYFEDIDYLTARLKLDPSMQ
GLMAYKMCSMMTEVLPPVRVLYLSAKTREGFEDLETLAYEHYC
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain1yr7 Chain A 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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PDB1yr7 Structural insights into a new homodimeric self-activated GTPase family.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		G10 G12 K13 T14 T15 D101 N165 K166 D168 L169 S223 A224
Binding residue
(residue number reindexed from 1)		G11 G13 K14 T15 T16 D102 N166 K167 D169 L170 S224 A225
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity

View graph for
Molecular Function
External links
PDB RCSB:1yr7, PDBe:1yr7, PDBj:1yr7
PDBsum1yr7
PubMed17468740
UniProtQ9UYR9|GPN_PYRAB GPN-loop GTPase PAB0955 (Gene Name=PYRAB14380)

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