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Structural evidence for a constrained conformation of short CDR-L3 in antibodies
Alexey Teplyakov1, Galina Obmolova, Thomas J Malia
1Janssen Research & Development, LLC, Spring House, Pennsylvania, 19477.
Abstract:
Three Fab structures used as targets in the Antibody Modeling Assessment presented a challenge for modeling CDR-L3 due to deviations from the most typical canonical structure. In all three antibodies CDR-L3 has eight residues, which is one residue shorter than usual, and has a conformation that is rarely observed in crystal structures. We analyzed the sequence and structural determinants of this conformation and found that the "short" CDR-L3 is remarkably rigid and retains the conformation in the interactions with antigens and neighboring CDRs.
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