4F8U image
Deposition Date 2012-05-18
Release Date 2012-08-15
Last Version Date 2024-03-20
Entry Detail
PDB ID:
4F8U
Keywords:
RNA/ANTIBIOTIC
Title:
Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (C2 form)
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.00 Å
R-Value Free:
0.26
R-Value Work:
0.25
Space Group:
C 1 2 1
4F8U validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
Chain IDs:A
Chain Length:22
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
Chain IDs:B
Chain Length:21
Number of Molecules:1
Biological Source:
Ligand Molecules
SIS
Primary Citation
Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site.
Acs Med.Chem.Lett. 3 741 744 (2012)
PMID: 24900542 DOI: 10.1021/ml300145y

Abstact

Sisomicin with an unsaturated sugar ring I displays better antibacterial activity than other structurally related aminoglycosides, such as gentamicin, tobramycin, and amikacin. In the present study, we have confirmed by X-ray analyses that the binding mode of sisomicin is basically similar but not identical to that of the related compounds having saturated ring I. A remarkable difference is found in the stacking interaction between ring I and G1491. While the typical saturated ring I with a chair conformation stacks on G1491 through CH/π interactions, the unsaturated ring I of sisomicin with a partially planar conformation can share its π-electron density with G1491 and fits well within the A-site helix.

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Primary Citation of related structures
4F8V