Structure of PDB 7abz Chain 6 Binding Site BS03

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 IDKIR
InChIInChI=1S/C43H60N2O12/c1-9-11-13-21-31-42(6,7)38(50)39(51)43(54,57-31)28(10-2)40(52)44-23-17-16-19-26(4)36(55-8)27(5)37-35(49)34(48)30(56-37)20-15-12-14-18-25(3)33(47)32-29(46)22-24-45-41(32)53/h9,11-22,24,27-28,30-31,34-39,48-51,54H,10,23H2,1-8H3,(H,44,52)(H2,45,46,53)/b11-9-,14-12+,17-16+,20-15+,21-13+,25-18+,26-19+/t27-,28-,30-,31+,34+,35+,36-,37+,38+,39-,43-/m1/s1
InChIKeyHMSYAPGFKGSXAJ-PAHGNTJYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCC(C(=O)NCC=CC=C(C)C(C(C)C1C(C(C(O1)C=CC=CC=C(C)C(=O)C2=C(C=CNC2=O)O)O)O)OC)C3(C(C(C(C(O3)C=CC=CC)(C)C)O)O)O
CACTVS 3.341CC[CH](C(=O)NCC=CC=C(C)[CH](OC)[CH](C)[CH]1O[CH](C=CC=CC=C(C)C(=O)C2=C(O)C=CNC2=O)[CH](O)[CH]1O)[C]3(O)O[CH](C=CC=CC)C(C)(C)[CH](O)[CH]3O
CACTVS 3.341CC[C@H](C(=O)NC/C=C/C=C(C)/[C@@H](OC)[C@@H](C)[C@@H]1O[C@H](/C=C/C=C/C=C(C)/C(=O)C2=C(O)C=CNC2=O)[C@H](O)[C@@H]1O)[C@@]3(O)O[C@@H](\C=C\C=C/C)C(C)(C)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0CC[C@H](C(=O)NC\C=C\C=C(/C)\[C@H]([C@@H](C)[C@H]1[C@H]([C@H]([C@H](O1)\C=C\C=C\C=C(/C)\C(=O)C2=C(C=CNC2=O)O)O)O)OC)[C@@]3([C@@H]([C@@H](C([C@@H](O3)\C=C\C=C/C)(C)C)O)O)O
ACDLabs 10.04O=C1NC=CC(O)=C1C(=O)\C(=C\C=C\C=C\C2OC(C(O)C2O)C(C)C(OC)C(=C\C=C\CNC(=O)C(CC)C3(O)OC(\C=C\C=C/C)C(C(O)C3O)(C)C)\C)C
FormulaC43 H60 N2 O12
NameKIRROMYCIN;
MOCIMYCIN;
DELVOMYCIN;
MYC-8003
ChEMBL
DrugBank
ZINC
PDB chain7abz Chain 6 Residue 401 [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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PDB7abz Structures of tmRNA and SmpB as they transit through the ribosome.
Resolution3.21 Å
Binding residue
(original residue number in PDB)		I92 R123 Q124 V125 Y160 D161 D314 E315 R373 F374 A375 G384 A385
Binding residue
(residue number reindexed from 1)		I70 R101 Q102 V103 Y138 D139 D292 E293 R351 F352 A353 G362 A363
Annotation score1
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
View graph for
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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