Structure of PDB 1yrb Chain B Binding Site BS02

Receptor Information
>1yrb Chain B (length=260) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRGSHHHHHHGMASMIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLD
TGVKELPYEPSIDVREFVTVEEIMREGYGPNGAIVESYDRLMEKFNEYLN
KILRLEKENDYVLIDTPGQMETFLFHEFGVRLMENLPYPLVVYISDPEIL
KKPNDYCFVRFFALLIDLRLGATTIPALNKVDLLSEEEKERHRKYFEDID
YLTARLKLDPSMQGLMAYKMCSMMTEVLPPVRVLYLSAKTREGFEDLETL
AYEHYCTCGD
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 chain1yrb Chain B Residue 402 [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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PDB1yrb Structural insights into a new homodimeric self-activated GTPase family.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		G10 G12 K13 T14 T15 N165 K166 D168 L169 S223 A224 K225
Binding residue
(residue number reindexed from 1)		G24 G26 K27 T28 T29 N179 K180 D182 L183 S237 A238 K239
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:1yrb, PDBe:1yrb, PDBj:1yrb
PDBsum1yrb
PubMed17468740
UniProtQ9UYR9|GPN_PYRAB GPN-loop GTPase PAB0955 (Gene Name=PYRAB14380)

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