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4e43

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[[Image:4e43.png|left|200px]]
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==HIV protease (PR) dimer with acetate in exo site and peptide in active site==
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<StructureSection load='4e43' size='340' side='right' caption='[[4e43]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4e43]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [http://en.wikipedia.org/wiki/Unidentified Unidentified]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3kf1 3kf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E43 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E43 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kf1|3kf1]]</td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 Human immunodeficiency virus 1])</td></tr>
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<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=4e43 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e43 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e43 RCSB], [http://www.ebi.ac.uk/pdbsum/4e43 PDBsum]</span></td></tr>
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<table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.
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Fragment-based screen against HIV protease.,Perryman AL, Zhang Q, Soutter HH, Rosenfeld R, McRee DE, Olson AJ, Elder JE, Stout CD Chem Biol Drug Des. 2010 Mar;75(3):257-68. Epub 2010 Jan 19. PMID:20659109<ref>PMID:20659109</ref>
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The line below this paragraph, containing "STRUCTURE_4e43", creates the "Structure Box" on the page.
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{{STRUCTURE_4e43| PDB=4e43 | SCENE= }}
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===HIV protease (PR) dimer with acetate in exo site and peptide in active site===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_20659109}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 20659109 is the PubMed ID number.
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</StructureSection>
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{{ABSTRACT_PUBMED_20659109}}
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==About this Structure==
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[[4e43]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [http://en.wikipedia.org/wiki/Unidentified Unidentified]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3kf1 3kf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E43 OCA].
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==Reference==
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<ref group="xtra">PMID:020659109</ref><references group="xtra"/>
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[[Category: Human immunodeficiency virus 1]]
[[Category: Human immunodeficiency virus 1]]
[[Category: Unidentified]]
[[Category: Unidentified]]

Revision as of 07:46, 5 June 2014

HIV protease (PR) dimer with acetate in exo site and peptide in active site

4e43, resolution 1.54Å

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