1yx9: Difference between revisions

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-{{Seed}}
-[[Image:1yx9.png|left|200px]]
-<!--
+==Effect of Dimethyl Sulphoxide on the crystal structure of Porcine Pepsin==
-The line below this paragraph, containing "STRUCTURE_1yx9", creates the "Structure Box" on the page.
+<StructureSection load='1yx9' size='340' side='right'caption='[[1yx9]], [[Resolution|resolution]] 3.00&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'>[[1yx9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YX9 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>
-{{STRUCTURE_1yx9|  PDB=1yx9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yx9 OCA], [https://pdbe.org/1yx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yx9 RCSB], [https://www.ebi.ac.uk/pdbsum/1yx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yx9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PEPA_PIG PEPA_PIG] Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent.
+== 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/yx/1yx9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1yx9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of porcine pepsin crystallized in the presence of dimethyl sulphoxide has been analysed by X-ray crystallography to obtain insights into the structural events that occur at the onset of chemical denaturation of proteins. The results show that one dimethyl sulphoxide molecule occupies a site on the surface of pepsin interacting with two of its residues. An increase in the average temperature factor of pepsin in the presence of dimethyl sulphoxide has been observed indicating protein destabilization induced by the denaturant. Significant increase in the temperature factor and weakening of the electron density have been observed for the catalytic water molecule located between the active aspartates. The conformation of pepsin remains unchanged in the crystal structure. However, the enzyme assay and circular dichroism studies indicate that dimethyl sulphoxide causes a slight change in the secondary structure and complete loss of activity of pepsin in solution.
-===Effect of Dimethyl Sulphoxide on the crystal structure of Porcine Pepsin===
+Effect of dimethyl sulphoxide on the crystal structure of porcine pepsin.,Kesavulu MM, Ramasubramanian S, Suguna K Biochem Biophys Res Commun. 2005 Jun 17;331(4):1510-4. PMID:15883044<ref>PMID:15883044</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1yx9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15883044}}, adds the Publication Abstract to the page
+*[[Pepsin|Pepsin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15883044 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15883044}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-YX9 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YX9 OCA].
-==Reference==
-<ref group="xtra">PMID:15883044</ref><references group="xtra"/>
-[[Category: Pepsin A]]
 [[Category: Sus scrofa]]
-[[Category: Kesavulu, M M.]]
+[[Category: Kesavulu MM]]
-[[Category: Ramasubramanian, S.]]
+[[Category: Ramasubramanian S]]
-[[Category: Suguna, K.]]
+[[Category: Suguna K]]
-[[Category: Dimethyl sulphoxide]]
-[[Category: Pepsin]]
-[[Category: Protein denaturation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:49:58 2009''