1pq5: Difference between revisions

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-[[Image:1pq5.jpg|left|200px]]
- {{Structure
+==Trypsin at pH 5, 0.85 A==
-|PDB= 1pq5 |SIZE=350|CAPTION= <scene name='initialview01'>1pq5</scene>, resolution 0.85&Aring;
+<StructureSection load='1pq5' size='340' side='right'caption='[[1pq5]], [[Resolution|resolution]] 0.85&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<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>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.85&#8491;</td></tr>
-|GENE=
+<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>
-|DOMAIN=
+<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>
-|RELATEDENTRY=[[1fn8|1FN8]], [[1fy4|1FY4]], [[1fy5|1FY5]], [[1gdn|1GDN]], [[1gdq|1GDQ]], [[1ppz|1PPZ]], [[1pq7|1PQ7]], [[1pq8|1PQ8]], [[1pqa|1PQA]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pq5 OCA], [http://www.ebi.ac.uk/pdbsum/1pq5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pq5 RCSB]</span>
+== 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/1pq5_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=1pq5 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 at pH 5, 0.85 A'''
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1pq5" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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 3D structures|Trypsin 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-PQ5 is a [[Single protein]] structure of sequence from [http://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].
+__TOC__
+</StructureSection>
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/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: catalysis]]
-[[Category: serine protease]]
-[[Category: trypsin]]
-[[Category: ultra-high resolution]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:03:05 2008''