Structure of PDB 1ha3 Chain B Binding Site BS01

Receptor Information
>1ha3 Chain B (length=379) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GEFIRTKPHVNVGTIGHVDHGKTTLTAALTFVTAAENPNAHVEYETAKRH
YSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQV
GVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSAL
LALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVE
DVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKT
LQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKE
EGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIK
PVALEEGLRFAIREGGRTVGAGVVTKILE
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 chain1ha3 Chain B Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ha3 Conformational Change of Elongation Factor TU Induced by Antibiotic Binding: Crystal Structure of the Complex between EF-TU:Gdp and Aurodox
Resolution2.0 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 N110 K111 D113 M114 S148 L150
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) D21 K24 T25 H85
Catalytic site (residue number reindexed from 1) D19 K22 T23 H59
Enzyme Commision number 3.1.5.1: dGTPase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ha3, PDBe:1ha3, PDBj:1ha3
PDBsum1ha3
PubMed11278992
UniProtQ5SHN6|EFTU1_THET8 Elongation factor Tu-A (Gene Name=tufA)

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