1ppz: Difference between revisions

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

OCA

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-[[Image:1ppz.gif|left|200px]]<br /><applet load="1ppz" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ppz, resolution 1.23&Aring;" />
-'''Trypsin complexes at atomic and ultra-high resolution'''<br />
-==Overview==
+==Trypsin complexes at atomic and ultra-high resolution==
-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.
+<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 [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='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='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='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>
+</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>
+    <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=1ppz ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-PPZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PPZ OCA].
+*[[Trypsin 3D structures|Trypsin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12937176 12937176]
 [[Category: Fusarium oxysporum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Trypsin]]
+[[Category: Jelsch C]]
-[[Category: Jelsch, C.]]
+[[Category: Lamzin VS]]
-[[Category: Lamzin, V.S.]]
+[[Category: Rypniewski W]]
-[[Category: Rypniewski, W.]]
+[[Category: Schmidt A]]
-[[Category: Schmidt, A.]]
-[[Category: SO4]]
-[[Category: atomic and ultra-high resolution]]
-[[Category: complex]]
-[[Category: dfp]]
-[[Category: serine protease]]
-[[Category: trypsin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:00:50 2007''