2f4t: Difference between revisions

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 ==Asite RNA + designer antibiotic==
-<StructureSection load='2f4t' size='340' side='right' caption='[[2f4t]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='2f4t' size='340' side='right'caption='[[2f4t]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2f4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F4T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2f4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F4T FirstGlance]. <br>
-</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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4t OCA], [https://pdbe.org/2f4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f4t RCSB], [https://www.ebi.ac.uk/pdbsum/2f4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f4t ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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<ref>PMID:16492561</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2f4t" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Haddad, J]]
+[[Category: Large Structures]]
-[[Category: Lentzen, G]]
+[[Category: Haddad J]]
-[[Category: Meroueh, S O]]
+[[Category: Lentzen G]]
-[[Category: Mobashery, S]]
+[[Category: Meroueh SO]]
-[[Category: Murray, J B]]
+[[Category: Mobashery S]]
-[[Category: Russell, R J]]
+[[Category: Murray JB]]
-[[Category: Asite rna]]
+[[Category: Russell RJ]]
-[[Category: Designer antibiotic]]
-[[Category: Rna]]