3ikc

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{{STRUCTURE_3ikc| PDB=3ikc | SCENE= }}
 
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===Structure of S67-27 in Complex with Kdo(2.8)-7-O-methyl-Kdo===
 
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{{ABSTRACT_PUBMED_19767317}}
 
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==About this Structure==
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==Structure of S67-27 in Complex with Kdo(2.8)-7-O-methyl-Kdo==
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[[3ikc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKC OCA].
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<StructureSection load='3ikc' size='340' side='right'caption='[[3ikc]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3ikc]] is a 4 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=3IKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKC FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=KME:(1E)-PROP-1-EN-1-YL+3-DEOXY-7-O-METHYL-ALPHA-D-MANNO-OCT-2-ULOPYRANOSIDONIC+ACID'>KME</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ikc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikc OCA], [https://pdbe.org/3ikc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikc RCSB], [https://www.ebi.ac.uk/pdbsum/3ikc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikc ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikc_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3ikc ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In order to explore the structural basis for adaptability in near germline monoclonal antibodies (mAb), we have examined the specificity of the promiscuous mAb S67-27 to both naturally derived carbohydrate antigens and a variety of synthetic nonnatural antigens based on the bacterial lipopolysaccharide component 3-deoxy-alpha-D-manno-oct-2-ulosonic acid (Kdo). One such analog, a 7-O-methyl (7-O-Me) Kdo disaccharide, was found to bind to the antibody with at least 30-fold higher affinity than any other antigen tested. The structure of S67-27 in complex with this analog and three other naturally occurring Kdo antigens revealed that the enhanced affinity of the mAb for the synthetic analog was accomplished by the strategic positioning of CDR H3 away from a conserved Kdo binding pocket that allowed the formation of new antibody-antigen contacts. Furthermore, the comparison of this structure with the structures of related mAbs revealed how the position and structure of CDR H3 influence the specificity or promiscuity of near-germline carbohydrate-recognizing antibodies by altering the architecture of the combining site.
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==Reference==
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The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.,Brooks CL, Blackler RJ, Sixta G, Kosma P, Muller-Loennies S, Brade L, Hirama T, MacKenzie CR, Brade H, Evans SV Glycobiology. 2010 Feb;20(2):138-47. Epub 2009 Sep 18. PMID:19767317<ref>PMID:19767317</ref>
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<ref group="xtra">PMID:019767317</ref><references group="xtra"/>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ikc" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Blackler, R J.]]
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[[Category: Blackler RJ]]
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[[Category: Brooks, C L.]]
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[[Category: Brooks CL]]
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[[Category: Evans, S V.]]
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[[Category: Evans SV]]
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[[Category: Antibody]]
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[[Category: Carbohydrate]]
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[[Category: Chlamydia]]
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[[Category: Fab]]
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[[Category: Immune system]]
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[[Category: Kdo]]
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[[Category: Lp]]
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Current revision

Structure of S67-27 in Complex with Kdo(2.8)-7-O-methyl-Kdo

PDB ID 3ikc

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