2f4s: Difference between revisions

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==A-site RNA in complex with neamine==
==A-site RNA in complex with neamine==
<StructureSection load='2f4s' size='340' side='right' caption='[[2f4s]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='2f4s' size='340' side='right'caption='[[2f4s]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2f4s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F4S FirstGlance]. <br>
<table><tr><td colspan='2'>[[2f4s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F4S FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XXX:(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL'>XXX</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]] 2.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2f4t|2f4t]], [[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=XXX:(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL'>XXX</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=2f4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f4s RCSB], [http://www.ebi.ac.uk/pdbsum/2f4s PDBsum]</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=2f4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4s OCA], [https://pdbe.org/2f4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f4s RCSB], [https://www.ebi.ac.uk/pdbsum/2f4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f4s ProSAT]</span></td></tr>
</table>
</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>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</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: A-site rna]]
[[Category: Russell RJ]]
[[Category: Neamine]]
[[Category: Rna]]

Latest revision as of 12:21, 14 February 2024

A-site RNA in complex with neamineA-site RNA in complex with neamine

Structural highlights

2f4s is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

2f4s, resolution 2.80Å

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