Structure of PDB 7abz Chain 6 Binding Site BS04

Receptor Information
>7abz Chain 6 (length=371) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGNTSHVEYDTP
TRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLG
RQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRG
SALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISG
RGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGE
NVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPF
FKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGL
RFAIREGGRTVGAGVVAKVLS
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 chain7abz Chain 6 Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7abz Structures of tmRNA and SmpB as they transit through the ribosome.
Resolution3.21 Å
Binding residue
(original residue number in PDB)		V20 D21 G23 K24 T25 K136 S173 A174 L175
Binding residue
(residue number reindexed from 1)		V20 D21 G23 K24 T25 K114 S151 A152 L153
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:7abz, PDBe:7abz, PDBj:7abz
PDBsum7abz
PubMed34389707
UniProtP0CE48|EFTU2_ECOLI Elongation factor Tu 2 (Gene Name=tufB)

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