6dn3: Difference between revisions
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==CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA== | ==CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA== | ||
<StructureSection load='6dn3' size='340' side='right' caption='[[6dn3]], [[Resolution|resolution]] 2.80Å' scene=''> | <StructureSection load='6dn3' size='340' side='right'caption='[[6dn3]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6dn3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DN3 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6dn3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum Fusobacterium nucleatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DN3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GZ4:7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium'>GZ4</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.8Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GZ4:7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium'>GZ4</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6dn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dn3 OCA], [https://pdbe.org/6dn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dn3 RCSB], [https://www.ebi.ac.uk/pdbsum/6dn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dn3 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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==See Also== | ==See Also== | ||
*[[Riboswitch|Riboswitch]] | *[[Riboswitch 3D structures|Riboswitch 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Batey | [[Category: Fusobacterium nucleatum]] | ||
[[Category: Berman | [[Category: Large Structures]] | ||
[[Category: Blount | [[Category: Batey RT]] | ||
[[Category: Coish | [[Category: Berman J]] | ||
[[Category: Gadwood | [[Category: Blount KF]] | ||
[[Category: Kaur | [[Category: Coish P]] | ||
[[Category: Kells | [[Category: Gadwood R]] | ||
[[Category: Mondragon | [[Category: Kaur H]] | ||
[[Category: Reyes | [[Category: Kells K]] | ||
[[Category: Schostarez | [[Category: Mondragon E]] | ||
[[Category: Suto | [[Category: Reyes FE]] | ||
[[Category: Vicens | [[Category: Schostarez H]] | ||
[[Category: Wickens | [[Category: Suto RK]] | ||
[[Category: Wilson | [[Category: Vicens Q]] | ||
[[Category: Wickens P]] | |||
[[Category: Wilson J]] | |||
Latest revision as of 09:09, 11 October 2023
CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNACRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA
Structural highlights
Publication Abstract from PubMedThe flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative -5FDQD- that protects mice against diarrhea-causing Clostridium difficile bacteria. Here, we present the structure-based drug design strategy that led to the discovery of this fluoro-phenyl derivative with antibacterial properties. This approach involved the following stages: (1) structural analysis of all available free and bound FMN riboswitch structures; (2) design, synthesis and purification of derivatives; (3) in vitro testing for productive binding using two chemical probing methods; (4) in vitro transcription termination assays; (5) resolution of the crystal structures of the FMN riboswitch in complex with the most mature candidates. In the process, we delineated principles for productive binding to this riboswitch, thereby demonstrating the effectiveness of a coordinated structure-guided approach to designing drugs against RNA. Structure-activity relationship of flavin analogs that target the FMN riboswitch.,Vicens Q, Mondragon E, Reyes FE, Coish P, Aristoff P, Berman J, Kaur H, Kells KW, Wickens P, Wilson J, Gadwood RC, Schostarez HJ, Suto RK, Blount KF, Batey RT ACS Chem Biol. 2018 Aug 14. doi: 10.1021/acschembio.8b00533. PMID:30107111[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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