2d03: Difference between revisions

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<StructureSection load='2d03' size='340' side='right'caption='[[2d03]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
<StructureSection load='2d03' size='340' side='right'caption='[[2d03]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d03]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D03 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2d03]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. 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>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
</td></tr><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>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1t2q|1t2q]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t2q|1t2q]]</div></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d03 OCA], [http://pdbe.org/2d03 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d03 RCSB], [http://www.ebi.ac.uk/pdbsum/2d03 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d03 ProSAT]</span></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=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>
</table>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
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==See Also==
==See Also==
*[[Antibody 3D structures|Antibody 3D structures]]
*[[Antibody 3D structures|Antibody 3D structures]]
*[[Sandbox 20009|Sandbox 20009]]
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
== References ==
== References ==
<references/>
<references/>

Revision as of 13:24, 8 December 2021

Crystal structure of the G91S mutant of the NNA7 FabCrystal structure of the G91S mutant of the NNA7 Fab

Structural highlights

2d03 is a 2 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. Xie K, Song SC, Spitalnik SL, Wedekind JE. Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition. Acta Crystallogr D Biol Crystallogr. 2005 Oct;61(Pt 10):1386-94. Epub 2005, Sep 28. PMID:16204891 doi:10.1107/S0907444905023851

2d03, resolution 1.97Å

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