Structure of PDB 5i4r Chain D Binding Site BS01

Receptor Information
>5i4r Chain D (length=335) Species: 469008 (Escherichia coli BL21(DE3)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAAT
DGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLS
QYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDK
PFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGV
EMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEV
YILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKM
VVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG
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 chain5i4r Chain C Residue 101 [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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PDB5i4r Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		N136 K137 D139 M140 S174 L176
Binding residue
(residue number reindexed from 1)		N77 K78 D80 M81 S115 L117
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T62 H85
Catalytic site (residue number reindexed from 1) T3 H26
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006414 translational elongation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5i4r, PDBe:5i4r, PDBj:5i4r
PDBsum5i4r
PubMed28973472
UniProtP0CE47|EFTU1_ECOLI Elongation factor Tu 1 (Gene Name=tufA)

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