2aj5: Difference between revisions
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{{Theoretical_model}} | {{Theoretical_model}} | ||
==3D STRUCTURE OF THE SUBSTRATE-BOUND SARS CHYMOTRYPSIN-LIKE CYSTEINE PROTEINASE== | |||
<StructureSection load='2aj5' size='340' side='right'caption='[[2aj5]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AJ5 FirstGlance]. <br> | |||
</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=2aj5 FirstGlance], [https://www.ebi.ac.uk/pdbsum/2aj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aj5 ProSAT]</span></td></tr> | |||
-- | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Severe acute respiratory syndrome (SARS) is a contagious and deadly disease caused by a new coronavirus. The protein sequence of the chymotrypsin-like cysteine proteinase (CCP) responsible for SARS viral replication has been identified as a target for developing anti-SARS drugs. Here, I report the ATVRLQ(p1)A(p1')-bound CCP 3D model predicted by 420 different molecular dynamics simulations (2.0 ns for each simulation with a 1.0-fs time step). This theoretical model was released at the Protein Data Bank (PDB; code: 1P76) before the release of the first X-ray structure of CCP (PDB code: 1Q2W). In contrast to the catalytic dyad observed in X-ray structures of CCP and other coronavirus cysteine proteinases, a catalytic triad comprising Asp187, His41, and Cys145 is found in the theoretical model of the substrate-bound CCP. The simulations of the CCP complex suggest that substrate binding leads to the displacement of a water molecule entrapped by Asp187 and His41, thus converting the dyad to a more efficient catalytic triad. The CCP complex structure has an expanded active-site pocket that is useful for anti-SARS drug design. In addition, this work demonstrates that multiple molecular dynamics simulations are effective in correcting errors that result from low-sequence-identity homology modeling. | |||
Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding.,Pang YP Proteins. 2004 Dec 1;57(4):747-57. PMID:15690493<ref>PMID:15690493</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2aj5" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Theoretical Model]] | ||
[[Category: Large Structures]] | |||
== | |||
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[[Category: Pang, Y.-P]] | [[Category: Pang, Y.-P]] | ||
Latest revision as of 14:41, 17 November 2021
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3D STRUCTURE OF THE SUBSTRATE-BOUND SARS CHYMOTRYPSIN-LIKE CYSTEINE PROTEINASE
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