2F4U image
Deposition Date 2005-11-24
Release Date 2006-05-02
Last Version Date 2024-02-14
Entry Detail
PDB ID:
2F4U
Keywords:
RNA
Title:
Asite RNA + designer antibiotic
Biological Source:
Source Organism:
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.60 Å
R-Value Free:
0.29
R-Value Work:
0.25
R-Value Observed:
0.29
Space Group:
P 21 21 21
2F4U validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
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'
Chain IDs:A, B
Chain Length:21
Number of Molecules:2
Biological Source:
Ligand Molecules
AB6
Primary Citation
Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site
Chem.Biol. 13 129 138 (2006)
PMID: 16492561 DOI: 10.1016/j.chembiol.2005.11.004

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures
2F4S
2F4T
2F4V