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Canonical structures of short CDR-L3 in antibodies.

Teplyakov A, Gilliland GL - Proteins (2014)

Bottom Line: Their correct identification is essential for successful prediction of antibody structure.This in turn requires regular updates of the classification of canonical structures to match the expanding experimental database.We have analyzed all crystal structures of Fab and Fv with the eight-residue CDR-L3 and identified three major canonical structures covering 82% of a nonredundant set.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Center of Excellence, Janssen Research and Development, LLC, Spring House, Pennsylvania, 19477.

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Related in: MedlinePlus

Electron density (2Fo-Fc omit map contoured at 1.2 RMSD) for CDR-L3 with the correct conformation shown in green. A: 1t4k.11 B: 2xtj.12
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fig03: Electron density (2Fo-Fc omit map contoured at 1.2 RMSD) for CDR-L3 with the correct conformation shown in green. A: 1t4k.11 B: 2xtj.12

Mentions: Two members of the group, 1t4k11 and 2xtj,12 were assigned to L3-8-P7 after certain corrections in the models. Both structures deposited in the PDB show peptide 93–94 flipped with respect to the canonical structure resulting in the “LP” conformation for residues 94–96. However, inspection of the electron density maps indicates that both models should be corrected (Fig. 3). In addition to the peptide flip, Gly93 in 2xtj should be modeled in the trans rather than cis configuration. This and other examples emphasize the need of a curated structural database free of errors that could be used for structure classifications and as a template source for antibody modeling.


Canonical structures of short CDR-L3 in antibodies.

Teplyakov A, Gilliland GL - Proteins (2014)

Electron density (2Fo-Fc omit map contoured at 1.2 RMSD) for CDR-L3 with the correct conformation shown in green. A: 1t4k.11 B: 2xtj.12
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4260120&req=5

fig03: Electron density (2Fo-Fc omit map contoured at 1.2 RMSD) for CDR-L3 with the correct conformation shown in green. A: 1t4k.11 B: 2xtj.12
Mentions: Two members of the group, 1t4k11 and 2xtj,12 were assigned to L3-8-P7 after certain corrections in the models. Both structures deposited in the PDB show peptide 93–94 flipped with respect to the canonical structure resulting in the “LP” conformation for residues 94–96. However, inspection of the electron density maps indicates that both models should be corrected (Fig. 3). In addition to the peptide flip, Gly93 in 2xtj should be modeled in the trans rather than cis configuration. This and other examples emphasize the need of a curated structural database free of errors that could be used for structure classifications and as a template source for antibody modeling.

Bottom Line: Their correct identification is essential for successful prediction of antibody structure.This in turn requires regular updates of the classification of canonical structures to match the expanding experimental database.We have analyzed all crystal structures of Fab and Fv with the eight-residue CDR-L3 and identified three major canonical structures covering 82% of a nonredundant set.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Center of Excellence, Janssen Research and Development, LLC, Spring House, Pennsylvania, 19477.

Show MeSH
Related in: MedlinePlus