2fcm: Difference between revisions
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==X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin with a Cubic Space Group== | ==X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin with a Cubic Space Group== | ||
<StructureSection load='2fcm' size='340' side='right' caption='[[2fcm]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='2fcm' size='340' side='right'caption='[[2fcm]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2fcm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FCM OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[2fcm]] 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=2FCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FCM FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | ||
<tr id=' | <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=DGN:D-GLUTAMINE'>DGN</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=2fcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fcm OCA], [https://pdbe.org/2fcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fcm RCSB], [https://www.ebi.ac.uk/pdbsum/2fcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fcm ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/2fcm_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/2fcm_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
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==See Also== | ==See Also== | ||
*[[ | *[[3D structures of ubiquitin|3D structures of ubiquitin]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Bang D]] | ||
[[Category: | [[Category: Gribenko AV]] | ||
[[Category: | [[Category: Kent SB]] | ||
[[Category: | [[Category: Kossiakoff AA]] | ||
[[Category: | [[Category: Makhatadze GI]] | ||
[[Category: | [[Category: Tereshko V]] | ||
Latest revision as of 10:59, 30 October 2024
X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin with a Cubic Space GroupX-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin with a Cubic Space Group
Structural highlights
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 PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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