Figure 4.

Superimposition of chains 1z6t-A and 2a5y-B. Both chains are not superimposeable as a whole, although the constituting domains have considerable structural similarities (Figure 3b). The TopMatch algorithm (11) provides several solutions (alternative alignments) for the comparison of two protein structures, which is most auxiliary in the current example where chains have undergone major conformational changes. (a) Alignment with c1z6tA2 and c1z6tA3 superimposed on domains c2a5yB2 and c2a5yB3. (b) Alternative alignment, showing structural equivalences of c1z6tA1 (red) and domain c2a5yB1 (orange) while the chains remain in the superimposition displayed in Figure 4a.