Structure of PDB 1efm Chain A Binding Site BS01

Receptor Information
>1efm Chain A (length=158) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNVGTIGHVDHGKTTLTAAITTVLAKTYTINTSHVEYDTPTRHYAHVDCP
GHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIV
FLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDA
EWEAKILE
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 chain1efm Chain A Residue 395 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1efm Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		V20 D21 G23
Binding residue
(residue number reindexed from 1)		V9 D10 G12
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D21 K24 T25 T61 H84
Catalytic site (residue number reindexed from 1) D10 K13 T14 T29 H52
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006412 translation
GO:0006414 translational elongation
GO:0046677 response to antibiotic
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0032045 guanyl-nucleotide exchange factor complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1efm, PDBe:1efm, PDBj:1efm
PDBsum1efm
PubMed3898365
UniProtP0CE48|EFTU2_ECOLI Elongation factor Tu 2 (Gene Name=tufB)

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