2F4U

Asite RNA + designer antibiotic

2F4U の概要

• エントリーDOI: 10.2210/pdb2f4u/pdb
• 関連するPDBエントリー: 2F4S 2F4T 2F4V
• 分子名称: 5'-R(*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-4-[(2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-{2-[(3-AMINOPROPYL)AMINO]ETHOXY}-3-HYDROXYCYCLOHEXYL)-2-HYDROXYBUTANAMIDE (3 entities in total)
• 機能のキーワード: asite rna, designer antibiotic, rna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 14010.76

構造登録者

Murray, J.B.,Meroueh, S.O.,Russell, R.J.,Lentzen, G.,Haddad, J.,Mobashery, S. (登録日: 2005-11-24, 公開日: 2006-05-02, 最終更新日: 2024-02-14)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.6 Å)