2d03: Difference between revisions

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{{Seed}}
[[Image:2d03.png|left|200px]]


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==Crystal structure of the G91S mutant of the NNA7 Fab==
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<StructureSection load='2d03' size='340' side='right'caption='[[2d03]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2d03]] 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=2D03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D03 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]] 1.97&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
{{STRUCTURE_2d03|  PDB=2d03  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d03 OCA], [https://pdbe.org/2d03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d03 RCSB], [https://www.ebi.ac.uk/pdbsum/2d03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d03 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/d0/2d03_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2d03 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The NNA7 Fab antibody fragment recognizes the human N-type blood-group antigen comprised of the N-terminal glycopeptide of glycophorin A (GPA). A mutant form of this Fab fragment, NNA7-G91S, exhibits markedly reduced antigen binding. To provide insight into how these Fab fragments recognize this glycopeptide antigen, the crystal structures of NNA7 and NNA7-G91S were solved and refined to 1.83 and 1.97 A resolution, respectively. Both molecules are composed of the same heavy (H) chain Fd fragment, but each contains a slightly different light (L) chain owing to the G91S substitution. Specifically, the G91S mutation pushes the backbone of the neighboring H chain away from complementarity-determining region 3 (CDR3) of the L-chain variable region, allowing an additional glycerol cryoprotectant molecule to enter the antigen-combining site near the putative location of O-linked glycosylation. Each Fab fragment also possesses a well defined 2-(N-morpholino)ethanesulfonic acid (MES) molecule trapped in its antigen-combining site, as well as a crystallographic symmetry-related molecule comprising an amino-acid sequence that is virtually identical to the N-terminus of GPA. The MES molecule interacts with the H-chain CDR in a manner reminiscent of antibody-carbohydrate complexes. These results suggest a model for recognition of the glycopeptide antigen that accounts for the deleterious effect of the G91S substitution.


===Crystal structure of the G91S mutant of the NNA7 Fab===
Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.,Xie K, Song SC, Spitalnik SL, Wedekind JE Acta Crystallogr D Biol Crystallogr. 2005 Oct;61(Pt 10):1386-94. Epub 2005, Sep 28. PMID:16204891<ref>PMID:16204891</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2d03" style="background-color:#fffaf0;"></div>


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==See Also==
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*[[Antibody 3D structures|Antibody 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 16204891 is the PubMed ID number.
*[[Sandbox 20009|Sandbox 20009]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
{{ABSTRACT_PUBMED_16204891}}
== References ==
 
<references/>
==About this Structure==
__TOC__
2D03 is a 2 chains structure of 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=2D03 OCA].
</StructureSection>
 
[[Category: Large Structures]]
==Reference==
<ref group="xtra">PMID:16204891</ref><ref group="xtra">PMID:15039587</ref><references group="xtra"/>
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Song, S C.]]
[[Category: Song SC]]
[[Category: Spitalnik, S L.]]
[[Category: Spitalnik SL]]
[[Category: Wedekind, J E.]]
[[Category: Wedekind JE]]
[[Category: Xie, K.]]
[[Category: Xie K]]
[[Category: Antibody]]
 
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