Structure of PDB 1yr8 Chain A Binding Site BS01

Receptor Information
>1yr8 Chain A (length=246) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASMIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLDTGVKELPYEPSI
DVREFVTVEEIMREGYGPNGAIVESYDRLMEKFNEYLNKILRLEKENDYV
LIDTPGQMETFLFHEFGVRLMENLPYPLVVYISDPEILKKPNDYCFVRFF
ALLIDLRLGATTIPALNKVDLLSEEEKERHRKYFEDIDYLTARLKLDPSM
QGLMAYKMCSMMTEVLPPVRVLYLSAKTREGFEDLETLAYEHYCTC
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 chain1yr8 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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PDB1yr8 Structural insights into a new homodimeric self-activated GTPase family.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A9 G10 G12 K13 T14 T15 K166 D168 L169 S223 A224 K225
Binding residue
(residue number reindexed from 1)		A11 G12 G14 K15 T16 T17 K168 D170 L171 S225 A226 K227
Annotation score4
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:1yr8, PDBe:1yr8, PDBj:1yr8
PDBsum1yr8
PubMed17468740
UniProtQ9UYR9|GPN_PYRAB GPN-loop GTPase PAB0955 (Gene Name=PYRAB14380)

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