3ijy

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{{Seed}}
 
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[[Image:3ijy.png|left|200px]]
 
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==Structure of S67-27 in Complex with Kdo(2.8)Kdo==
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The line below this paragraph, containing "STRUCTURE_3ijy", creates the "Structure Box" on the page.
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<StructureSection load='3ijy' size='340' side='right'caption='[[3ijy]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3ijy]] 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=3IJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IJY FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.85&#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=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_3ijy| PDB=3ijy | SCENE= }}
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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=3ijy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ijy OCA], [https://pdbe.org/3ijy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ijy RCSB], [https://www.ebi.ac.uk/pdbsum/3ijy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ijy 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/ij/3ijy_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=3ijy 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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===Structure of S67-27 in Complex with Kdo(2.8)Kdo===
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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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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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The line below this paragraph, {{ABSTRACT_PUBMED_19767317}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3ijy" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19767317 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19767317}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3IJY is a 4 chains structure with sequences 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=3IJY OCA].
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==Reference==
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<ref group="xtra">PMID:19767317</ref><references group="xtra"/>
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[[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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:49:16 2010''
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Current revision

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

PDB ID 3ijy

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