1nd3: Difference between revisions

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-[[Image:1nd3.png|left|200px]]
+==The structure of HRV16, when complexed with pleconaril, an antiviral compound==
+<StructureSection load='1nd3' size='340' side='right' caption='[[1nd3]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND3 FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W11:3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE'>W11</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1na1|1na1]], [[1ncq|1ncq]], [[1ncr|1ncr]], [[1nd2|1nd2]]</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd3 PDBsum]</span></td></tr>
+<table>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1nd3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of human rhinovirus 16 (HRV16) and HRV14 are incubated with pleconaril, drug occupancy in the binding pocket is lower than when pleconaril is introduced during assembly prior to crystallization. This effect is far more marked in HRV16 than in HRV14 and is more marked with pleconaril than with other compounds. These observations are consistent with virus yield inhibition studies and radiolabeled drug binding studies showing that the antiviral effect of pleconaril against HRV16 is greater on the infectivity of progeny virions than the parent input viruses. These data suggest that drug integration into the binding pocket during assembly, or at some other late stage in virus replication, may contribute to the antiviral activity of capsid binding compounds.
-{{STRUCTURE_1nd3|  PDB=1nd3  |  SCENE=  }}
+Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds.,Zhang Y, Simpson AA, Ledford RM, Bator CM, Chakravarty S, Skochko GA, Demenczuk TM, Watanyar A, Pevear DC, Rossmann MG J Virol. 2004 Oct;78(20):11061-9. PMID:15452226<ref>PMID:15452226</ref>
-===The structure of HRV16, when complexed with pleconaril, an antiviral compound===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_15452226}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[1nd3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_a16 Human rhinovirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND3 OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:015452226</ref><references group="xtra"/>
 [[Category: Human rhinovirus a16]]
 [[Category: Bator, C M.]]