View source for 6hbx


==The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with ethylguanidine==
<StructureSection load='6hbx' size='340' side='right'caption='[[6hbx]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6hbx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloeobacter_violaceus Gloeobacter violaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HBX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.54&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBV:5-BROMOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CBV</scene>, <scene name='pdbligand=EGD:N-ETHYLGUANIDINE'>EGD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6hbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hbx OCA], [https://pdbe.org/6hbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hbx RCSB], [https://www.ebi.ac.uk/pdbsum/6hbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hbx ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a ten-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands have potential applications in chemical biology.

Structure-guided design of a high affinity ligand for a riboswitch.,Huang L, Wang J, Wilson TJ, Lilley DMJ RNA. 2019 Jan 4. pii: rna.069567.118. doi: 10.1261/rna.069567.118. PMID:30609994<ref>PMID:30609994</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6hbx" style="background-color:#fffaf0;"></div>

==See Also==
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Gloeobacter violaceus]]
[[Category: Large Structures]]
[[Category: Huang L]]
[[Category: Lilley DMJ]]