2xo0: Difference between revisions

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-[[Image:2xo0.jpg|left|200px]]
-<!--
+==xpt-pbuX C74U Riboswitch from B. subtilis bound to 24-diamino-1,3,5- triazine identified by virtual screening==
-The line below this paragraph, containing "STRUCTURE_2xo0", creates the "Structure Box" on the page.
+<StructureSection load='2xo0' size='340' side='right'caption='[[2xo0]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2xo0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XO0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XO0 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=ZZS:1,3,5-TRIAZINE-2,4-DIAMINE'>ZZS</scene></td></tr>
-{{STRUCTURE_2xo0|  PDB=2xo0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xo0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xo0 OCA], [https://pdbe.org/2xo0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xo0 RCSB], [https://www.ebi.ac.uk/pdbsum/2xo0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xo0 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The increasing number of RNA crystal structures enables a structure-based approach to the discovery of new RNA-binding ligands. To develop the poorly explored area of RNA-ligand docking, we have conducted a virtual screening exercise for a purine riboswitch to probe the strengths and weaknesses of RNA-ligand docking. Using a standard protein-ligand docking program with only minor modifications, four new ligands with binding affinities in the micromolar range were identified, including two compounds based on molecular scaffolds not resembling known ligands. RNA-ligand docking performed comparably to protein-ligand docking indicating that this approach is a promising option to explore the wealth of RNA structures for structure-based ligand design.
-===XPT-PBUX C74U RIBOSWITCH FROM B. SUBTILIS BOUND TO 24-DIAMINO-1,3,5-TRIAZINE IDENTIFIED BY VIRTUAL SCREENING===
+Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking.,Daldrop P, Reyes FE, Robinson DA, Hammond CM, Lilley DM, Batey RT, Brenk R Chem Biol. 2011 Mar 25;18(3):324-35. PMID:21439477<ref>PMID:21439477</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2xo0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21439477}}, adds the Publication Abstract to the page
+*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21439477 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21439477}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus subtilis]]
-[[2xo0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XO0 OCA].
+[[Category: Large Structures]]
+[[Category: Batey RT]]
-==Reference==
+[[Category: Brenk R]]
-<ref group="xtra">PMID:21439477</ref><references group="xtra"/>
+[[Category: Daldrop P]]
-[[Category: Batey, R T.]]
+[[Category: Hammond CM]]
-[[Category: Brenk, R.]]
+[[Category: Lilley DMJ]]
-[[Category: Daldrop, P.]]
+[[Category: Reyes FE]]
-[[Category: Hammond, C M.]]
+[[Category: Robinson DA]]
-[[Category: Lilley, D M.J.]]
-[[Category: Reyes, F E.]]
-[[Category: Robinson, D A.]]