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==Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18==
<StructureSection load='4h20' size='340' side='right'caption='[[4h20]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4h20]] 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=4H20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H20 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]] 1.9&#8491;</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=4h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h20 OCA], [https://pdbe.org/4h20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h20 RCSB], [https://www.ebi.ac.uk/pdbsum/4h20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h20 ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
BACKGROUND: Many antibody crystal structures have been solved. Structural modeling programs have been developed that utilize this information to predict 3-D structures of an antibody based upon its sequence. Because of the problem of self-reference, the accuracy and utility of these predictions can only be tested when a new structure has not yet been deposited in the Protein Data Bank. METHODS: We have solved the crystal structure of the Fab fragment of RAC18, a protective anti-ricin mAb, to 1.9 A resolution. We have also modeled the Fv structure of RAC18 using publicly available Ab modeling tools Prediction of Immunoglobulin Structures (PIGS), RosettaAntibody, and Web Antibody Modeling (WAM). The model structures underwent energy minimization. We compared results to the crystal structure on the basis of root-mean-square deviation (RMSD), template modeling score (TM-score), Z-score, and MolProbity analysis. FINDINGS: The crystal structure showed a pocket formed mainly by AA residues in each of the heavy chain complementarity determining regions (CDRs). There were differences between the crystal structure and structures predicted by the modeling tools, particularly in the CDRs. There were also differences among the predicted models, although the differences were small and within experimental error. No one modeling program was clearly superior to the others. In some cases, choosing structures based only on sequence homology to the crystallized Ab yielded RMSDs comparable to the models. CONCLUSIONS: Molecular modeling programs accurately predict the structure of most regions of antibody variable domains of RAC18. The hypervariable CDRs proved most difficult to model, particularly H chain CDR3. Because CDR3 is most often involved in contact with antigen, this defect must be considered when using models to identify potential contacts between antibody and antigen. Because this study represents only a single case, the results cannot be generalized. Rather they highlight the utility and limitations of modeling programs.

Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody.,Zhao Z, Worthylake D, Lecour L Jr, Maresh GA, Pincus SH PLoS One. 2012;7(12):e52613. doi: 10.1371/journal.pone.0052613. Epub 2012 Dec 19. PMID:23285112<ref>PMID:23285112</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 4h20" style="background-color:#fffaf0;"></div>

==See Also==
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: LeCour Jr LF]]
[[Category: Maresh G]]
[[Category: Pincus SH]]
[[Category: Worthylake DK]]
[[Category: Zhao Z]]