Structural evidence for a constrained conformation of short CDR-L3 in antibodies

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. (C) 2014 Wiley Periodicals, Inc.