Structure of PDB 5mi9 Chain B Binding Site BS01

Receptor Information
>5mi9 Chain B (length=379) Species: 331112 (Escherichia coli HS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKA
NTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAQMDGAILVVAATDGPMP
QTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFP
GDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLP
IEDVFSICGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRK
LLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSK
DEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLI
HPIAMDDGLRFAIREGGRTVGAGVVAKVL
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 chain5mi9 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mi9 Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		D22 G24 K25 T26 T27 N136 K137 D139 S174 A175 L176
Binding residue
(residue number reindexed from 1)		D14 G16 K17 T18 T19 N122 K123 D125 S160 A161 L162
Annotation score4
Enzymatic activity
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:5mi9, PDBe:5mi9, PDBj:5mi9
PDBsum5mi9
PubMed29546243
UniProtP0CE47|EFTU1_ECOLI Elongation factor Tu 1 (Gene Name=tufA)

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