Structure of PDB 4p3y Chain A Binding Site BS01

Receptor Information
>4p3y Chain A (length=386) Species: 469008 (Escherichia coli BL21(DE3)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKA
RGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAA
TDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELL
SQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAID
KPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTG
VEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESE
VYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIK
MVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG
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 chain4p3y Chain A Residue 402 [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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PDB4p3y Structure of the Acinetobacter baumannii Dithiol Oxidase DsbA Bound to Elongation Factor EF-Tu Reveals a Novel Protein Interaction Site.
Resolution2.154 Å
Binding residue
(original residue number in PDB)		D22 G24 K25 T26 T27 N136 K137 D139 M140 S174 L176
Binding residue
(residue number reindexed from 1)		D14 G16 K17 T18 T19 N128 K129 D131 M132 S166 L168
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D22 K25 T26 T62 H85
Catalytic site (residue number reindexed from 1) D14 K17 T18 T54 H77
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4p3y, PDBe:4p3y, PDBj:4p3y
PDBsum4p3y
PubMed24860094
UniProtP0CE47|EFTU1_ECOLI Elongation factor Tu 1 (Gene Name=tufA)

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