Comparison of the CDR2 and CDR3 regions of the MUC1-specific antibody SM3 and the MA TCR and modeling their interactions with MUC1. (A) Amino acid sequence alignment of SM3 and MA TCR. Numbering corresponds to MA TCR sequence. Residues in bold are hypothesized to be involved in the binding. (B-C) SM3 and (D-E) MA TCR computer-based models of the interactions with the MUC1 epitope. The colors indicate the following: red, CDR1; green, CDR2; blue, CDR3; yellow, MUC1; white, the SM3 light chain and MA TCR α chain; gray, the SM3 heavy chain and MA TCR β chain. Contact residues are shown as stick diagrams with nitrogens in blue and oxygens in red, in close-up comparison of SM3 (C) and MA TCR (E) computer-based models of their interactions with MUC1 and labeled by chain, residue, and number in chain.