title: 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.
authors.affiliation: Biotechnology Center of Excellence, Janssen Research and Development, LLC, Spring House, Pennsylvania, 19477.
authors.forename: Alexey
authors.initials: A
authors.lastname: Teplyakov
authors.forename: Gary L
authors.initials: GL
authors.lastname: Gilliland
mesh_terms: D000818:Animals; D000906:Antibodies / Q000737:chemistry*; D022801:Complementarity Determining Regions / Q000737:chemistry*; D030562:Databases, Protein; D006801:Humans; D007128:Immunoglobulin Fragments / Q000737:chemistry; D007147:Immunoglobulin Light Chains / Q000737:chemistry*; D007135:Immunoglobulin Variable Region / Q000737:chemistry*; D051379:Mice; D008958:Models, Molecular; D011487:Protein Conformation; D051381:Rats
chemical_list: D000906:Antibodies; D022801:Complementarity Determining Regions; D007128:Immunoglobulin Fragments; D007147:Immunoglobulin Light Chains; D007135:Immunoglobulin Variable Region
keywords: CDR conformation; canonical structure; cis-isomer; crystal structure; structure prediction