3dcr: Difference between revisions

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{{Seed}}
[[Image:3dcr.jpg|left|200px]]


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==X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor==
The line below this paragraph, containing "STRUCTURE_3dcr", creates the "Structure Box" on the page.
<StructureSection load='3dcr' size='340' side='right'caption='[[3dcr]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3dcr]] 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=3DCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DCR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=KVS:N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-ACETYL-L-THREONYL)AMINO]-3-METHYLPENT-4-ENOYL}AMINO)-2-BUTYL-4,4-DIHYDROXYNONANOYL]-L-GLUTAMINYL-L-ARGININAMIDE'>KVS</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
{{STRUCTURE_3dcr|  PDB=3dcr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dcr OCA], [https://pdbe.org/3dcr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dcr RCSB], [https://www.ebi.ac.uk/pdbsum/3dcr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dcr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O38732_9HIV1 O38732_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/dc/3dcr_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=3dcr 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.


===X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3dcr" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18657969}}, adds the Publication Abstract to the page
*[[Immunodeficiency virus protease 3D structures|Immunodeficiency virus protease 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18657969 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18657969}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Human immunodeficiency virus 1]]
3DCR is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DCR OCA].
[[Category: Large Structures]]
 
[[Category: Kent SBH]]
==Reference==
[[Category: Mandal K]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/18657969 18657969]
[[Category: Terechko VA]]
[[Category: HIV-1 retropepsin]]
[[Category: Torbeev VY]]
[[Category: Protein complex]]
[[Category: Kent, S B.H.]]
[[Category: Mandal, K.]]
[[Category: Terechko, V A.]]
[[Category: Torbeev, V Y.]]
[[Category: Beta-strand]]
[[Category: Beta-turn]]
[[Category: Hiv-1 protease]]
[[Category: Homodimer]]
[[Category: Hydrolase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 12:14:59 2008''

Latest revision as of 15:07, 1 November 2023

X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor

3dcr, resolution 1.40Å

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