3dcr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:07, 1 November 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3dcr.png|left|200px]]
 
-
<!--
+
==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>
-
<!--
+
==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 3 chains 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]]
-
<ref group="xtra">PMID:18657969</ref><references group="xtra"/>
+
[[Category: Terechko VA]]
-
[[Category: HIV-1 retropepsin]]
+
[[Category: Torbeev VY]]
-
[[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 Tue Feb 17 13:47:46 2009''
+

Current revision

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

PDB ID 3dcr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3dcr"
Personal tools