2fcn: Difference between revisions

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-[[Image:2fcn.png|left|200px]]
-<!--
+==X-ray Crystal Structure of a Chemically Synthesized [D-Val35]Ubiquitin with a Cubic Space Group==
-The line below this paragraph, containing "STRUCTURE_2fcn", creates the "Structure Box" on the page.
+<StructureSection load='2fcn' size='340' side='right'caption='[[2fcn]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2fcn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FCN FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene></td></tr>
-{{STRUCTURE_2fcn|  PDB=2fcn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcn OCA], [https://pdbe.org/2fcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fcn RCSB], [https://www.ebi.ac.uk/pdbsum/2fcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcn ProSAT]</span></td></tr>
+</table>
+== 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/fc/2fcn_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=2fcn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The alpha-helix is a fundamental protein structural motif and is frequently terminated by a glycine residue. Explanations for the predominance of glycine at the C-cap terminal portions of alpha-helices have invoked uniquely favorable energetics of this residue in a left-handed conformation or enhanced solvation of the peptide backbone because of the absence of a side chain. Attempts to quantify the contributions of these two effects have been made previously, but the issue remains unresolved. Here we have used chemical protein synthesis to dissect the energetic basis of alpha-helix termination by comparing a series of ubiquitin variants containing an L-amino acid or the corresponding D-amino acid at the C-cap Gly35 position. D-Amino acids can adopt a left-handed conformation without energetic penalty, so the contributions of conformational strain and backbone solvation can thus be separated. Analysis of the thermodynamic data revealed that the preference for glycine at the C' position of a helix is predominantly a conformational effect.
-===X-ray Crystal Structure of a Chemically Synthesized [D-Val35]Ubiquitin with a Cubic Space Group===
+Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.,Bang D, Gribenko AV, Tereshko V, Kossiakoff AA, Kent SB, Makhatadze GI Nat Chem Biol. 2006 Mar;2(3):139-43. Epub 2006 Jan 30. PMID:16446709<ref>PMID:16446709</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16446709}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2fcn" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16446709 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16446709}}
-==About this Structure==
-[[2fcn]] is a 2 chain structure of [[Ubiquitin]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCN OCA].
 ==See Also==
-*[[Ubiquitin]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:16446709</ref><references group="xtra"/>
+__TOC__
-[[Category: Bang, D.]]
+</StructureSection>
-[[Category: Gribenko, A V.]]
+[[Category: Homo sapiens]]
-[[Category: Kent, S B.]]
+[[Category: Large Structures]]
-[[Category: Kossiakoff, A A.]]
+[[Category: Bang D]]
-[[Category: Makhatadze, G I.]]
+[[Category: Gribenko AV]]
-[[Category: Tereshko, V.]]
+[[Category: Kent SB]]
-[[Category: Structural protein]]
+[[Category: Kossiakoff AA]]
-[[Category: Ubiquitin]]
+[[Category: Makhatadze GI]]
+[[Category: Tereshko V]]