Structure of PDB 4pc3 Chain B Binding Site BS01

Receptor Information
>4pc3 Chain B (length=372) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGKARGITINTSHVEYDT
PTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILL
GRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVR
GSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSIS
GRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAG
ENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTP
FFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDG
LRFAIREGGRTVGAGVVAKVLG
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 chain4pc3 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4pc3 Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.
Resolution1.8313 Å
Binding residue
(original residue number in PDB)		D21 G23 K24 T25 T26 N135 K136 M139 S173 A174 L175
Binding residue
(residue number reindexed from 1)		D14 G16 K17 T18 T19 N114 K115 M118 S152 A153 L154
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H22 K24 T25 T61 H84
Catalytic site (residue number reindexed from 1) H15 K17 T18 T40 H63
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4pc3, PDBe:4pc3, PDBj:4pc3
PDBsum4pc3
PubMed26073967
UniProtP0CE47|EFTU1_ECOLI Elongation factor Tu 1 (Gene Name=tufA)

[Back to BioLiP]