Figure 1
Structural analysis of the BC2-Nb/BC2T complex.
(a) BC2-Nb/BC2T backbone interactions. The BC2-peptide (BC2T) (pink) folds into a β-strand that is part of a β-sheet structure formed by the complementarity determining region 3 (CDR3, blue) and framework regions 2 and 3 (FR2 and FR3, grey). Shown are 13 backbone-backbone hydrogen bonds (black dashed lines) of which one is mediated by water (red sphere). The CDR3 contributes eight and the framework regions five of these interactions. The CDR1 (light yellow) and CDR2 (yellow) are not participating in binding. (b) “Headlock” interaction. A charge-mediated interaction between Arg106 of the CDR3 (blue) and Glu44 in FR2 is stabilizing the BC2-Nb/BC2T complex. These amino acid side chains are reaching over the peptide (pink), forming a salt bridge that locks the peptide into its binding site. (c) Specific BC2-Nb/BC2T interactions. In addition to the backbone interactions, a small number of interactions mediated by side chains generate specificity for the BC2T peptide sequence. BC2T residue W10 is involved in a CH-π interaction with Cys50 (dotted line). A water (red sphere) is bound by peptide S8 (pink), Tyr109, two carbonyl groups and one amine group. The charge-mediated interaction between Arg106 (CDR3) and the side chain of Glu44 (FR2), reaching over the peptide, is also shown.
