1plg: Difference between revisions
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New page: left|200px<br /><applet load="1plg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1plg, resolution 2.8Å" /> '''EVIDENCE FOR THE EXTE... |
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== | ==EVIDENCE FOR THE EXTENDED HELICAL NATURE OF POLYSACCHARIDE EPITOPES. THE 2.8 ANGSTROMS RESOLUTION STRUCTURE AND THERMODYNAMICS OF LIGAND BINDING OF AN ANTIGEN BINDING FRAGMENT SPECIFIC FOR ALPHA-(2->8)-POLYSIALIC ACID== | ||
The antigen binding fragment from an IgG2a kappa murine monoclonal | <StructureSection load='1plg' size='340' side='right'caption='[[1plg]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1plg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PLG FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</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=1plg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1plg OCA], [https://pdbe.org/1plg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1plg RCSB], [https://www.ebi.ac.uk/pdbsum/1plg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1plg ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A2NHM3_MOUSE A2NHM3_MOUSE] | |||
== 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/pl/1plg_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=1plg ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The antigen binding fragment from an IgG2a kappa murine monoclonal antibody with specificity for alpha-(2-->8)-linked sialic acid polymers has been prepared and crystallized in the absence of hapten. Crystals were grown by vapor diffusion equilibrium with 16-18% polyethylene glycol 4000 solutions. The structure was solved by molecular replacement methods and refined to a conventional R factor of 0.164 for data to 2.8 A. The binding site is observed to display a shape and distribution of charges that is complementary to that of the predicted conformation of the oligosaccharide epitope. A thermodynamic description of ligand binding has been compiled for oligosaccharides ranging in length from 9 to 41 residues, and the data for the largest ligand has been used in a novel way to estimate the size of the antigen binding site. A model of antigen binding is presented that satisfies this thermodynamic data, as well as a previously reported requirement of conformational specificity of the oligosaccharide. X-ray crystallographic and thermodynamic evidence are consistent with a binding site that accommodates at least eight sialic acid residues. | |||
Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 A resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for alpha-(2-->8)-polysialic acid.,Evans SV, Sigurskjold BW, Jennings HJ, Brisson JR, To R, Tse WC, Altman E, Frosch M, Weisgerber C, Kratzin HD, et al. Biochemistry. 1995 May 23;34(20):6737-44. PMID:7538787<ref>PMID:7538787</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1plg" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
[[Category: Altman E]] | |||
[[Category: Altman | [[Category: Bitter-Suermann D]] | ||
[[Category: Bitter-Suermann | [[Category: Brisson J-R]] | ||
[[Category: Brisson | [[Category: Bundle DR]] | ||
[[Category: Bundle | [[Category: Evans SV]] | ||
[[Category: Evans | [[Category: Frosch M]] | ||
[[Category: Frosch | [[Category: Jennings HJ]] | ||
[[Category: Jennings | [[Category: Klebert S]] | ||
[[Category: Klebert | [[Category: Kratzin H]] | ||
[[Category: Kratzin | [[Category: Rose DR]] | ||
[[Category: Rose | [[Category: Sigurskjold BW]] | ||
[[Category: Sigurskjold | [[Category: To R]] | ||
[[Category: To | [[Category: Tse WC]] | ||
[[Category: Tse | [[Category: Vaesen M]] | ||
[[Category: Vaesen | [[Category: Weisgerber C]] | ||
[[Category: Weisgerber | [[Category: Young NM]] | ||
[[Category: Young | |||
