2nnk: Difference between revisions

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-[[Image:2nnk.png|left|200px]]
-{{STRUCTURE_2nnk|  PDB=2nnk  |  SCENE=  }}
+==Crystal structure analysis of HIV-1 protease mutant I84V with a inhibitor saquinavir==
+<StructureSection load='2nnk' size='340' side='right'caption='[[2nnk]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2nnk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NNK 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]] 1.25&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ROC:(2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT-BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3-HYDROXY-1-PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE'>ROC</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=2nnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nnk OCA], [https://pdbe.org/2nnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nnk RCSB], [https://www.ebi.ac.uk/pdbsum/2nnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nnk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7SSI0_9HIV1 Q7SSI0_9HIV1]
+== 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/nn/2nnk_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/main_output.php?pdb_ID=2nnk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Saquinavir (SQV), the first antiviral HIV-1 protease (PR) inhibitor approved for AIDS therapy, has been studied in complexes with PR and the variants PR(I) (84V) and PR(V) (82A) containing the single mutations I84V and V82A that provide resistance to all the clinical inhibitors. Atomic resolution crystal structures (0.97-1.25 A) of the SQV complexes were analyzed in comparison to the protease complexes with darunavir, a new drug that targets resistant HIV, in order to understand the molecular basis of drug resistance. PR(I) (84V) and PR(V) (82A) complexes were obtained in both the space groups P2(1)2(1)2 and P2(1)2(1)2(1), which provided experimental limits for the conformational flexibility. The SQV interactions with PR were very similar in the mutant complexes, consistent with the similar inhibition constants. The mutation from bigger to smaller amino acids allows more space to accommodate the large group at P1' of SQV, unlike the reduced interactions observed in darunavir complexes. The residues 79-82 have adjusted to accommodate the large hydrophobic groups of SQV, suggesting that these residues are intrinsically flexible and their conformation depends more on the nature of the inhibitor than on the mutations in this region. This analysis will assist with development of more effective antiviral inhibitors.
-===Crystal structure analysis of HIV-1 protease mutant I84V with a inhibitor saquinavir===
+Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir.,Tie Y, Kovalevsky AY, Boross P, Wang YF, Ghosh AK, Tozser J, Harrison RW, Weber IT Proteins. 2007 Apr 1;67(1):232-42. PMID:17243183<ref>PMID:17243183</ref>
-{{ABSTRACT_PUBMED_17243183}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2nnk" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2nnk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NNK OCA].
+*[[Immunodeficiency virus protease 3D structures|Immunodeficiency virus protease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017243183</ref><references group="xtra"/>
+__TOC__
-[[Category: HIV-1 retropepsin]]
+</StructureSection>
 [[Category: Human immunodeficiency virus 1]]
-[[Category: Boross, P.]]
+[[Category: Large Structures]]
-[[Category: Ghosh, A K.]]
+[[Category: Boross P]]
-[[Category: Harrison, R W.]]
+[[Category: Ghosh AK]]
-[[Category: Kovalevsky, A Y.]]
+[[Category: Harrison RW]]
-[[Category: Tie, Y.]]
+[[Category: Kovalevsky AY]]
-[[Category: Tozser, J.]]
+[[Category: Tie Y]]
-[[Category: Wang, Y F.]]
+[[Category: Tozser J]]
-[[Category: Weber, I T.]]
+[[Category: Wang YF]]
-[[Category: Dimer]]
+[[Category: Weber IT]]
-[[Category: Hiv-1 protease]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: I84v]]
-[[Category: Mutant]]