1y3f: Difference between revisions

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-[[Image:1y3f.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1y3f", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1y3f|  PDB=1y3f  |  SCENE=  }}
-'''Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 F69A mutant'''
+==Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 F69A mutant==
+<StructureSection load='1y3f' size='340' side='right'caption='[[1y3f]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1y3f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] and [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y3F FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=15P:POLYETHYLENE+GLYCOL+(N=34)'>15P</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=1y3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3f OCA], [https://pdbe.org/1y3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y3f RCSB], [https://www.ebi.ac.uk/pdbsum/1y3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUBT_BACAM SUBT_BACAM] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. Has a high substrate specificity to fibrin.<ref>PMID:12524032</ref>
+== 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/y3/1y3f_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=1y3f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin BPN', and for resistance of the inhibitor to proteolysis. These functional properties were investigated in tandem with the crystal structures of the mutant inhibitor-enzyme complexes. A dense hydrogen bonding network that supports the binding loop in the vicinity of the scissile bond was found to be important both for enzyme affinity and for stability to proteolysis. Structural analysis, in combination with biochemical measurements, allows differentiation of the structural components most important for resistance to proteolysis and/or binding. The most critical participating residues in the network were found to be Thr-58, Glu-60, Arg-65, and Gly-83. Glu-60 is more important for resistance to proteolysis than for binding, while Arg-65 and two other Arg residues play a greater role in binding than in resistance to proteolysis. Structural comparisons reveal a wide variety of subtle conformational changes in response to mutation, with built-in robustness in the hydrogen bond network, such that loss of one contact is compensated by other new contacts.
-==Overview==
+Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2.,Radisky ES, Lu CJ, Kwan G, Koshland DE Jr Biochemistry. 2005 May 10;44(18):6823-30. PMID:15865427<ref>PMID:15865427</ref>
-A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin BPN', and for resistance of the inhibitor to proteolysis. These functional properties were investigated in tandem with the crystal structures of the mutant inhibitor-enzyme complexes. A dense hydrogen bonding network that supports the binding loop in the vicinity of the scissile bond was found to be important both for enzyme affinity and for stability to proteolysis. Structural analysis, in combination with biochemical measurements, allows differentiation of the structural components most important for resistance to proteolysis and/or binding. The most critical participating residues in the network were found to be Thr-58, Glu-60, Arg-65, and Gly-83. Glu-60 is more important for resistance to proteolysis than for binding, while Arg-65 and two other Arg residues play a greater role in binding than in resistance to proteolysis. Structural comparisons reveal a wide variety of subtle conformational changes in response to mutation, with built-in robustness in the hydrogen bond network, such that loss of one contact is compensated by other new contacts.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Y3F is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] and [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3F OCA].
+</div>
+<div class="pdbe-citations 1y3f" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2., Radisky ES, Lu CJ, Kwan G, Koshland DE Jr, Biochemistry. 2005 May 10;44(18):6823-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15865427 15865427]
+*[[Chymotrypsin inhibitor 3D structures|Chymotrypsin inhibitor 3D structures]]
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus amyloliquefaciens]]
 [[Category: Hordeum vulgare]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Subtilisin]]
+[[Category: Koshland Jr DE]]
-[[Category: Jr., D E.Koshland.]]
+[[Category: Kwan G]]
-[[Category: Kwan, G.]]
+[[Category: Lu CJ]]
-[[Category: Lu, C J.]]
+[[Category: Radisky ES]]
-[[Category: Radisky, E S.]]
-[[Category: Inhibitor]]
-[[Category: Serine protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 15:50:12 2008''