Summary information and primary citation
- PDB-id
-
4f8v;
DSSR-derived features in text and
JSON formats
- Class
- RNA-antibiotic
- Method
- X-ray (2.8 Å)
- Summary
- Crystal structure of the bacterial ribosomal decoding
site in complex with sisomicin (p21212 form)
- Reference
-
Kondo J, Koganei M, Kasahara T (2012): "Crystal
structure and specific binding mode of sisomicin to the
bacterial ribosomal decoding site." Acs
Med.Chem.Lett., 3, 741-744. doi:
10.1021/ml300145y.
- Abstract
- 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.
