1pq5: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Trypsin at pH 5, 0.85 A== | ==Trypsin at pH 5, 0.85 A== | ||
<StructureSection load='1pq5' size='340' side='right' caption='[[1pq5]], [[Resolution|resolution]] 0.85Å' scene=''> | <StructureSection load='1pq5' size='340' side='right'caption='[[1pq5]], [[Resolution|resolution]] 0.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1pq5]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1pq5]] 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=1PQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PQ5 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.85Å</td></tr> | ||
<tr id=' | <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=1pq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pq5 OCA], [https://pdbe.org/1pq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pq5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pq5 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/TRYP_FUSOX TRYP_FUSOX] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pq/1pq5_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pq/1pq5_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=1pq5 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 26: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1pq5" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Trypsin|Trypsin]] | *[[Trypsin 3D structures|Trypsin 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 34: | Line 37: | ||
</StructureSection> | </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 03:22, 21 November 2024
Trypsin at pH 5, 0.85 ATrypsin at pH 5, 0.85 A
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
|
| ||||||||||||||||||