2foa: Difference between revisions
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< | ==Structure of porcine pancreatic elastase in 40/50/10 % benzene== | ||
<StructureSection load='2foa' size='340' side='right'caption='[[2foa]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2foa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FOA FirstGlance]. <br> | |||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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=2foa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2foa OCA], [https://pdbe.org/2foa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2foa RCSB], [https://www.ebi.ac.uk/pdbsum/2foa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2foa ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CELA1_PIG CELA1_PIG] Acts upon elastin. | |||
== 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/fo/2foa_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=2foa ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design. | |||
Multiple solvent crystal structures: probing binding sites, plasticity and hydration.,Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D J Mol Biol. 2006 Apr 14;357(5):1471-82. Epub 2006 Jan 30. PMID:16488429<ref>PMID:16488429</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2foa" style="background-color:#fffaf0;"></div> | |||
== | |||
==See Also== | ==See Also== | ||
*[[Elastase]] | *[[Elastase 3D structures|Elastase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Sus scrofa]] | [[Category: Sus scrofa]] | ||
[[Category: Bellamacina | [[Category: Bellamacina CR]] | ||
[[Category: Mattos | [[Category: Mattos C]] | ||
[[Category: Peisach | [[Category: Peisach E]] | ||
[[Category: Pereira | [[Category: Pereira A]] | ||
[[Category: Petsko | [[Category: Petsko GA]] | ||
[[Category: Ringe | [[Category: Ringe D]] | ||
[[Category: Vitkup | [[Category: Vitkup D]] | ||
Latest revision as of 12:07, 6 November 2024
Structure of porcine pancreatic elastase in 40/50/10 % benzeneStructure of porcine pancreatic elastase in 40/50/10 % benzene
Structural highlights
FunctionCELA1_PIG Acts upon elastin. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedMultiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design. Multiple solvent crystal structures: probing binding sites, plasticity and hydration.,Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D J Mol Biol. 2006 Apr 14;357(5):1471-82. Epub 2006 Jan 30. PMID:16488429[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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