3ecg: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3ecg.png|left|200px]]
+==High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065==
+<StructureSection load='3ecg' size='340' side='right' caption='[[3ecg]], [[Resolution|resolution]] 1.18&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ecg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ECG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ECG FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=065:(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(2S,3R)-3-HYDROXY-4-(N-ISOBUTYLBENZO[D][1,3]DIOXOLE-5-SULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE'>065</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ebz|3ebz]], [[3ec0|3ec0]]</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/HIV-2_retropepsin HIV-2 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.47 3.4.23.47] </span></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=3ecg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ecg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ecg RCSB], [http://www.ebi.ac.uk/pdbsum/3ecg 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/ec/3ecg_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 ==
+No drug has been targeted specifically for HIV-2 (human immunodeficiency virus type 2) infection despite its increasing prevalence worldwide. The antiviral HIV-1 (human immunodeficiency virus type 1) protease (PR) inhibitor darunavir and the chemically related GRL98065 and GRL06579A were designed with the same chemical scaffold and different substituents at P2 and P2' to optimize polar interactions for HIV-1 PR (PR1). These inhibitors are also effective antiviral agents for HIV-2-infected cells. Therefore, crystal structures of HIV-2 PR (PR2) complexes with the three inhibitors have been solved at 1.2-A resolution to analyze the molecular basis for their antiviral potency. Unusually, the crystals were grown in imidazole and zinc acetate buffer, which formed interactions with the PR2 and the inhibitors. Overall, the structures were very similar to the corresponding inhibitor complexes of PR1 with an RMSD of 1.1 A on main-chain atoms. Most hydrogen-bond and weaker C-H...O interactions with inhibitors were conserved in the PR2 and PR1 complexes, except for small changes in interactions with water or disordered side chains. Small differences were observed in the hydrophobic contacts for the darunavir complexes, in agreement with relative inhibition of the two PRs. These near-atomic-resolution crystal structures verify the inhibitor potency for PR1 and PR2 and will provide the basis for the development of antiviral inhibitors targeting PR2.
-{{STRUCTURE_3ecg|  PDB=3ecg  |  SCENE=  }}
+Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease.,Kovalevsky AY, Louis JM, Aniana A, Ghosh AK, Weber IT J Mol Biol. 2008 Dec 5;384(1):178-92. Epub 2008 Sep 20. PMID:18834890<ref>PMID:18834890</ref>
-===High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_18834890}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[3ecg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ECG OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:018834890</ref><references group="xtra"/>
 [[Category: HIV-2 retropepsin]]
 [[Category: Viruses]]
-[[Category: Kovalevsky, A Y.]]
+[[Category: Kovalevsky, A Y]]
-[[Category: Weber, I T.]]
+[[Category: Weber, I T]]
 [[Category: Aspartic protease]]
 [[Category: Hiv-2]]