3dck
From Proteopedia
(Difference between revisions)
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| - | + | ==X-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene isostere inhibitor== | |
| - | + | <StructureSection load='3dck' size='340' side='right' caption='[[3dck]], [[Resolution|resolution]] 1.80Å' scene=''> | |
| - | {{ | + | == Structural highlights == |
| + | <table><tr><td colspan='2'>[[3dck]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DCK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DCK FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KVI:(2S)-2-{[(2R,5S)-5-{[(2S,3S)-2-{[(2S,3R)-2-(ACETYLAMINO)-3-HYDROXYBUTANOYL]AMINO}-3-METHYLPENTANOYL]AMINO}-2-BUTYL-4-OXONONANOYL]AMINO}-N~1~-[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]PENTANEDIAMIDE'>KVI</scene></td></tr> | ||
| + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dcr|3dcr]]</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] </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=3dck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dck OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dck RCSB], [http://www.ebi.ac.uk/pdbsum/3dck 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/dc/3dck_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 == | ||
| + | Here we report the X-ray structures of chemically synthesized HIV-1 protease and the inactive [D25N]HIV-1 protease complexed with the ketomethylene isostere inhibitor Ac-Thr-Ile-Nle psi[CO-CH(2)]Nle-Gln-Arg.amide at 1.4 and 1.8A resolution, respectively. In complex with the active enzyme, the keto-group was found to be converted into the hydrated gem-diol, while the structure of the complex with the inactive D25N enzyme revealed an intact keto-group. These data support the general acid-general base mechanism for HIV-1 protease catalysis. | ||
| - | + | Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site.,Torbeev VY, Mandal K, Terechko VA, Kent SB Bioorg Med Chem Lett. 2008 Aug 15;18(16):4554-7. Epub 2008 Jul 15. PMID:18657969<ref>PMID:18657969</ref> | |
| - | + | ||
| - | == | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | + | </div> | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
[[Category: HIV-1 retropepsin]] | [[Category: HIV-1 retropepsin]] | ||
| - | [[Category: Kent, S B.H | + | [[Category: Kent, S B.H]] |
| - | [[Category: Mandal, K | + | [[Category: Mandal, K]] |
| - | [[Category: Terechko, V A | + | [[Category: Terechko, V A]] |
| - | [[Category: Torbeev, V Y | + | [[Category: Torbeev, V Y]] |
[[Category: Beta-strand]] | [[Category: Beta-strand]] | ||
[[Category: Beta-turn]] | [[Category: Beta-turn]] | ||
Revision as of 14:25, 18 December 2014
X-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene isostere inhibitor
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