1pq7: Difference between revisions
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==Trypsin at 0.8 A, pH5 / borax== | |||
<StructureSection load='1pq7' size='340' side='right'caption='[[1pq7]], [[Resolution|resolution]] 0.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1pq7]] 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=1PQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PQ7 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]] 0.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</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=1pq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pq7 OCA], [https://pdbe.org/1pq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pq7 RCSB], [https://www.ebi.ac.uk/pdbsum/1pq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pq7 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/pq/1pq7_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1pq7 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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1pq7" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Trypsin|Trypsin]] | *[[Trypsin 3D structures|Trypsin 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Fusarium oxysporum]] | [[Category: Fusarium oxysporum]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Jelsch | [[Category: Jelsch C]] | ||
[[Category: Lamzin | [[Category: Lamzin VS]] | ||
[[Category: Rypniewski | [[Category: Rypniewski W]] | ||
[[Category: Schmidt | [[Category: Schmidt A]] | ||
Latest revision as of 11:44, 6 November 2024
Trypsin at 0.8 A, pH5 / boraxTrypsin at 0.8 A, pH5 / borax
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedA 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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