2F4U: Asite Rna + Designer Antibiotic

The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.
PDB ID: 2F4UDownload
MMDB ID: 53123
PDB Deposition Date: 2005/11/24
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
Biological Unit for 2F4U: dimeric; determined by author
Molecular Components in 2F4U
Label Count Molecule
Nucleotide(1 molecule)
5'- R(*gp*cp*gp*up*cp*ap*cp*ap*cp*cp*gp*gp*up*gp*ap*ap*gp*up*cp *gp*c)-3'
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB