Structure of the Fab fragment of a monoclonal antibody specific for carcinoembryonic antigen

The three-dimensional structure of the Fab fragment of the murine monoclonal antibody A5B7, which is specific for carcinoembryonic antigen (CEA) a protein expressed on carcinoma cell surfaces, has been determined. The structure was solved by molecular replacement and has been refined to an R factor for 21.2% (all data 8-2.1 A). The conformation of the hypervariable loops, which form the antigen binding site, are consistent with canonical loop predictions. Hypervariable loop H3 is unusual in surface exposing many hydrophobic groups at the expense of burying an aspartic acid in the protein core. Other regions of the structure that influence the conformation of the binding site are identified. This structure forms a basis for analysing the effects of amino-acid substitutions in both hypervariable and framework regions in engineering studies of the A5B7 antibody.