2F4T

Asite RNA + designer antibiotic

Summary for 2F4T

• Entry DOI: 10.2210/pdb2f4t/pdb
• Related: 2F4S 2F4U 2F4V
• Descriptor: 5'-R(*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3', 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3', (2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE (3 entities in total)
• Functional Keywords: asite rna, designer antibiotic, rna
• Total number of polymer chains: 2
• Total formula weight: 14608.08

Authors

Murray, J.B.,Meroueh, S.O.,Russell, R.J.,Lentzen, G.,Haddad, J.,Mobashery, S. (deposition date: 2005-11-24, release date: 2006-05-02, Last modification date: 2024-02-14)

Primary citation

Murray, J.B.,Meroueh, S.O.,Russell, R.J.,Lentzen, G.,Haddad, J.,Mobashery, S.
Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site
Chem.Biol., 13:129-138, 2006

PubMed Abstract: 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.

PubMed: 16492561
DOI: 10.1016/j.chembiol.2005.11.004

Experimental method

X-RAY DIFFRACTION (3 Å)