1yu6: Difference between revisions

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-{{Seed}}
-[[Image:1yu6.png|left|200px]]
-<!--
+==Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex==
-The line below this paragraph, containing "STRUCTURE_1yu6", creates the "Structure Box" on the page.
+<StructureSection load='1yu6' size='340' side='right'caption='[[1yu6]], [[Resolution|resolution]] 1.55&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'>[[1yu6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis] and [https://en.wikipedia.org/wiki/Meleagris_gallopavo Meleagris gallopavo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YU6 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]] 1.55&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-{{STRUCTURE_1yu6|  PDB=1yu6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yu6 OCA], [https://pdbe.org/1yu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yu6 RCSB], [https://www.ebi.ac.uk/pdbsum/1yu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yu6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IOVO_MELGA IOVO_MELGA]
+== 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/yu/1yu6_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=1yu6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+One of the most studied protein proteinase inhibitors is the turkey ovomucoid third domain, OMTKY3. This inhibitor contains a reactive-site loop (Lys13I-Arg21I) that binds in a nearly identical manner to all studied serine proteinases, regardless of their clan or specificity. The crystal structure of OMTKY3 bound to subtilisin Carlsberg (CARL) has been determined. There are two complete copies of the complexes in the crystallographic asymmetric unit. Whereas the two enzyme molecules are virtually identical [0.16 A root-mean-square difference (r.m.s.d.) for 274 C(alpha) atoms], the two inhibitor molecules show dramatic differences between one another (r.m.s.d. = 2.4 A for 50 C(alpha) atoms). When compared with other proteinase-bound OMTKY3 molecules, these inhibitors show even larger differences. This work facilitates a re-evaluation of the importance of certain ovomucoid residues in proteinase binding and explains why additivity and sequence-based binding-prediction methods fail for the CARL-OMTKY3 complex.
-===Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex===
+Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.,Maynes JT, Cherney MM, Qasim MA, Laskowski M Jr, James MN Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):580-8. Epub 2005, Apr 20. PMID:15858268<ref>PMID:15858268</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1yu6" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15858268}}, adds the Publication Abstract to the page
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15858268 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15858268}}
+__TOC__
+</StructureSection>
-==About this Structure==
-YU6 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis] and [http://en.wikipedia.org/wiki/Meleagris_gallopavo Meleagris gallopavo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YU6 OCA].
-==Reference==
-Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations., Maynes JT, Cherney MM, Qasim MA, Laskowski M Jr, James MN, Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):580-8. Epub 2005, Apr 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15858268 15858268]
 [[Category: Bacillus licheniformis]]
+[[Category: Large Structures]]
 [[Category: Meleagris gallopavo]]
-[[Category: Protein complex]]
+[[Category: Cherney MM]]
-[[Category: Subtilisin]]
+[[Category: James MNG]]
-[[Category: Cherney, M M.]]
+[[Category: Laskowski Jr M]]
-[[Category: James, M N.G.]]
+[[Category: Maynes JT]]
-[[Category: Jr., M Laskowski.]]
+[[Category: Qasim MA]]
-[[Category: Maynes, J T.]]
-[[Category: Qasim, M A.]]
-[[Category: Protease]]
-[[Category: Protein proteinase inhibitor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:34:58 2008''