Canonical structures of short CDR-L3 in antibodies

Abstract

Despite sequence diversity, five out of six hypervariable loops in antibodies assume a limited number of conformations called canonical structures. 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. Antibodies with the eight-residue CDR-L3 represent the second most common type of antibodies after those with the nine-residue CDR-L3. 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. In most cases, the canonical structure is defined by the absence or presence and position of a proline residue within the CDR. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.