1ypa: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 ==DIRECT OBSERVATION OF BETTER HYDRATION AT THE N-TERMINUS OF AN ALPHA-HELIX WITH GLYCINE RATHER THAN ALANINE AS N-CAP==
-<StructureSection load='1ypa' size='340' side='right' caption='[[1ypa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1ypa' size='340' side='right'caption='[[1ypa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ypa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Barley Barley]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YPA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ypa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YPA FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ypa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ypa OCA], [http://pdbe.org/1ypa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ypa RCSB], [http://www.ebi.ac.uk/pdbsum/1ypa PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</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=1ypa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ypa OCA], [https://pdbe.org/1ypa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ypa RCSB], [https://www.ebi.ac.uk/pdbsum/1ypa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ypa ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ICI2_HORVU ICI2_HORVU]] Inhibits both subtilisin and chymotrypsin.
+[https://www.uniprot.org/uniprot/ICI2_HORVU ICI2_HORVU] Inhibits both subtilisin and chymotrypsin.
 == 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/yp/1ypa_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yp/1ypa_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 17: / Line 19: @@
 </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=1ypa ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structural basis for the stability of N termini of helices has been analyzed by thermodynamic and crystallographic studies of three suitably engineered mutants of the barley chymotrypsin inhibitor 2 with Ser, Gly, or Ala at the N-cap position (residue 31). Each mutant has a well-organized shell of hydration of the terminal NH groups of the helix. The three structures are virtually superimposable (rms separations for all atoms, including the common water molecules, are 0.15-0.17 A) and show neither changes in conformation at the site of substitution nor changes in the crystal packing. The only changes on going from Ser-31 to Ala-31 to Gly-31 are in the position of a water molecule (Wat-116). This is bound to the Ser-O gamma atom in the Ser-31 structure but is in a weak hydrogen bonding position with the NH of residue 34 (O ... N = 3.28 A) in the Ala-31 mutant, partly replacing the strong Ser-31-O gamma ... N34 hydrogen bond (O ... N = 2.65 A). The corresponding water molecule completely replaces the Ser hydroxyl hydrogen bond to N34 on mutation to Gly (2.74 A). The only other change between the three structures is an additional water molecule in the Ala-31 structure (Wat-150) that partly compensates for the weak Wat-116 ... N34 hydrogen bond. Perturbation of solvation by the side chain of Ala is consistent with earlier hypotheses on the importance of exposure of the termini of helices to the aqueous solvent.
-Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue.,Harpaz Y, Elmasry N, Fersht AR, Henrick K Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):311-5. PMID:8278384<ref>PMID:8278384</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ypa" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Chymotrypsin Inhibitor|Chymotrypsin Inhibitor]]
+*[[Chymotrypsin inhibitor 3D structures|Chymotrypsin inhibitor 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Barley]]
+[[Category: Hordeum vulgare]]
-[[Category: Elmasry, N]]
+[[Category: Large Structures]]
-[[Category: Fersht, A R]]
+[[Category: Elmasry N]]
-[[Category: Harpaz, Y]]
+[[Category: Fersht AR]]
-[[Category: Henrick, K]]
+[[Category: Harpaz Y]]
+[[Category: Henrick K]]