1pq8

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(New page: 200px<br /><applet load="1pq8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pq8, resolution 1.00&Aring;" /> '''Trypsin at pH 4 at a...)
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[[Image:1pq8.jpg|left|200px]]<br /><applet load="1pq8" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pq8, resolution 1.00&Aring;" />
 
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'''Trypsin at pH 4 at atomic resolution'''<br />
 
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==Overview==
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==Trypsin at pH 4 at atomic resolution==
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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.
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<StructureSection load='1pq8' size='340' side='right'caption='[[1pq8]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pq8]] is a 2 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=1PQ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PQ8 FirstGlance]. <br>
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</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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pq8 OCA], [https://pdbe.org/1pq8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pq8 RCSB], [https://www.ebi.ac.uk/pdbsum/1pq8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pq8 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TRYP_FUSOX TRYP_FUSOX]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pq/1pq8_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1pq8 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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1PQ8 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, LYS and CIT as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1PQ8 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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]
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</div>
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[[Category: Fusarium oxysporum]]
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<div class="pdbe-citations 1pq8" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Trypsin]]
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[[Category: Jelsch, C.]]
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[[Category: Lamzin, V.S.]]
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[[Category: Rypniewski, W.]]
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[[Category: Schmidt, A.]]
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[[Category: CIT]]
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[[Category: LYS]]
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[[Category: SO4]]
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[[Category: atomic resolution]]
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[[Category: catalysis]]
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[[Category: trypsin]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:01:16 2007''
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==See Also==
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*[[Trypsin 3D structures|Trypsin 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Fusarium oxysporum]]
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[[Category: Large Structures]]
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[[Category: Jelsch C]]
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[[Category: Lamzin VS]]
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[[Category: Rypniewski W]]
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[[Category: Schmidt A]]

Current revision

Trypsin at pH 4 at atomic resolution

PDB ID 1pq8

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