2f4t: Difference between revisions
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==Asite RNA + designer antibiotic== | ==Asite RNA + designer antibiotic== | ||
<StructureSection load='2f4t' size='340' side='right' caption='[[2f4t]], [[Resolution|resolution]] 3.00Å' scene=''> | <StructureSection load='2f4t' size='340' side='right' caption='[[2f4t]], [[Resolution|resolution]] 3.00Å' scene=''> | ||
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AB9:(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'>AB9</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AB9:(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'>AB9</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2f4s|2f4s]], [[2f4u|2f4u]], [[2f4v|2f4v]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2f4s|2f4s]], [[2f4u|2f4u]], [[2f4v|2f4v]]</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4t OCA], [http://pdbe.org/2f4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f4t RCSB], [http://www.ebi.ac.uk/pdbsum/2f4t PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4t OCA], [http://pdbe.org/2f4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f4t RCSB], [http://www.ebi.ac.uk/pdbsum/2f4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f4t ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
Revision as of 10:33, 18 October 2017
Asite RNA + designer antibioticAsite RNA + designer antibiotic
Structural highlights
Publication Abstract from PubMedThe 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. Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site.,Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S Chem Biol. 2006 Feb;13(2):129-38. PMID:16492561[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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