1ppz: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 ==Trypsin complexes at atomic and ultra-high resolution==
-<StructureSection load='1ppz' size='340' side='right' caption='[[1ppz]], [[Resolution|resolution]] 1.23&Aring;' scene=''>
+<StructureSection load='1ppz' size='340' side='right'caption='[[1ppz]], [[Resolution|resolution]] 1.23&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ppz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fusox Fusox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ppz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.23&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIS:MONOISOPROPYLPHOSPHORYLSERINE'>MIS</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MIS:MONOISOPROPYLPHOSPHORYLSERINE'>MIS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fn8|1fn8]], [[1fy4|1fy4]], [[1fy5|1fy5]], [[1gdq|1gdq]], [[1gdu|1gdu]], [[1gdn|1gdn]], [[1pq5|1pq5]], [[1pq7|1pq7]], [[1pq8|1pq8]], [[1pqa|1pqa]]</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=1ppz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppz OCA], [https://pdbe.org/1ppz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppz RCSB], [https://www.ebi.ac.uk/pdbsum/1ppz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppz ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppz OCA], [http://pdbe.org/1ppz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ppz RCSB], [http://www.ebi.ac.uk/pdbsum/1ppz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppz ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRYP_FUSOX TRYP_FUSOX]
 == 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/pp/1ppz_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/1ppz_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=1ppz ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion.
-Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis.,Schmidt A, Jelsch C, Ostergaard P, Rypniewski W, Lamzin VS J Biol Chem. 2003 Oct 31;278(44):43357-62. Epub 2003 Aug 22. PMID:12937176<ref>PMID:12937176</ref>
+==See Also==
+*[[Trypsin 3D structures|Trypsin 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ppz" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Fusox]]
+[[Category: Fusarium oxysporum]]
-[[Category: Trypsin]]
+[[Category: Large Structures]]
-[[Category: Jelsch, C]]
+[[Category: Jelsch C]]
-[[Category: Lamzin, V S]]
+[[Category: Lamzin VS]]
-[[Category: Rypniewski, W]]
+[[Category: Rypniewski W]]
-[[Category: Schmidt, A]]
+[[Category: Schmidt A]]
-[[Category: Atomic and ultra-high resolution]]
-[[Category: Complex]]
-[[Category: Dfp]]
-[[Category: Hydrolase]]
-[[Category: Serine protease]]