1fn6: Difference between revisions

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-[[Image:1fn6.jpg|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH 0.1% POLYDOCANOL==
-|PDB= 1fn6 |SIZE=350|CAPTION= <scene name='initialview01'>1fn6</scene>, resolution 1.8&Aring;
+<StructureSection load='1fn6' size='340' side='right'caption='[[1fn6]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1fn6]] 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=1FN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FN6 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]] 1.8&#8491;</td></tr>
-|GENE=
+<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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</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=1fn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fn6 OCA], [https://pdbe.org/1fn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fn6 RCSB], [https://www.ebi.ac.uk/pdbsum/1fn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fn6 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1qqu|1QQU]], [[1fmg|1FMG]], [[1fni|1FNI]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fn6 OCA], [http://www.ebi.ac.uk/pdbsum/1fn6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fn6 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/TRYP_PIG TRYP_PIG]
+== 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/fn/1fn6_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=1fn6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Polydocanol has a wide range of medical applications, especially in sclerotherapy of many diseases such as gastrointestinal antiplastia, oesophageal haemangioma etc. It is of interest to study the mode of binding of this medically important detergent and its subsequent action on proteins. Here, three crystal structures of serine protease trypsin are reported in the presence of varying concentrations of polydocanol in order to elucidate its mode of binding and interactions with proteins. Polydocanol binds to the protein with its hydrophilic head rather than the hydrophobic tail as is the case with other detergents such as SDS and MEGA-8. This hydrophilic binding mode results in the binding sites of polydocanol being distributed on the surface of the enzyme. There are at least 11 binding sites for polydocanol in trypsin. Polydocanol forms part of the large-scale water networks which connect distant regions of the enzyme, thereby stabilizing it. The hydrophilic binding of polydocanol also results in cross-linked pairs of trypsin molecules.
-'''CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH 0.1% POLYDOCANOL'''
+Structures of porcine beta-trypsin-detergent complexes: the stabilization of proteins through hydrophilic binding of polydocanol.,Deepthi S, Johnson A, Pattabhi V Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1506-12. Epub 2001, Oct 25. PMID:11679713<ref>PMID:11679713</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1fn6" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Polydocanol has a wide range of medical applications, especially in sclerotherapy of many diseases such as gastrointestinal antiplastia, oesophageal haemangioma etc. It is of interest to study the mode of binding of this medically important detergent and its subsequent action on proteins. Here, three crystal structures of serine protease trypsin are reported in the presence of varying concentrations of polydocanol in order to elucidate its mode of binding and interactions with proteins. Polydocanol binds to the protein with its hydrophilic head rather than the hydrophobic tail as is the case with other detergents such as SDS and MEGA-8. This hydrophilic binding mode results in the binding sites of polydocanol being distributed on the surface of the enzyme. There are at least 11 binding sites for polydocanol in trypsin. Polydocanol forms part of the large-scale water networks which connect distant regions of the enzyme, thereby stabilizing it. The hydrophilic binding of polydocanol also results in cross-linked pairs of trypsin molecules.
+*[[Trypsin 3D structures|Trypsin 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-FN6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FN6 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Structures of porcine beta-trypsin-detergent complexes: the stabilization of proteins through hydrophilic binding of polydocanol., Deepthi S, Johnson A, Pattabhi V, Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1506-12. Epub 2001, Oct 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11679713 11679713]
-[[Category: Single protein]]
 [[Category: Sus scrofa]]
-[[Category: Trypsin]]
+[[Category: Deepthi S]]
-[[Category: Deepthi, S.]]
+[[Category: Johnson A]]
-[[Category: Johnson, A.]]
+[[Category: Pattabhi V]]
-[[Category: Pattabhi, V.]]
-[[Category: hydrolase]]
-[[Category: serine protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:26:16 2008''