Structure of PDB 4v68 Chain AZ Binding Site BS04

Receptor Information
>4v68 Chain AZ (length=378) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GEFIRTKPHVNVGTIGHVDHGKTTLTAALTFVTAAENPAHVEYETAKRHY
SHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVG
VPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALL
ALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVED
VFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTL
QEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEE
GGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKP
VALEEGLRFAIREGGRTVGAGVVTKILE
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 chain4v68 Chain AZ Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4v68 GTPase activation of elongation factor EF-Tu by the ribosome during decoding
Resolution6.4 Å
Binding residue
(original residue number in PDB)		D21 G23 K24 T25 T26 N136 K137 D139 M140 S174 L176
Binding residue
(residue number reindexed from 1)		D19 G21 K22 T23 T24 N109 K110 D112 M113 S147 L149
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K24 T25 H85
Catalytic site (residue number reindexed from 1) K22 T23 H58
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4v68, PDBe:4v68, PDBj:4v68
PDBsum4v68
PubMed19229291
UniProtP60339|EFTU2_THET8 Elongation factor Tu-B (Gene Name=tufB)

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