Figure 4. The first principal component from PCA for the apo system.

The movement along the first principal component was shown in (a) and (b) for the two opposing (front and back) side views, and (c) for the top view. The two structures, colored blue and orange, correspond to the helices before and after the movement, respectively. The two monomers are distinguished by their different shades of color. This principal component closely corresponds to an overall relative rotation between the two monomers illustrated by the orange arrows with the blue plus sign marking the rotational direction in (c). The two inter-monomer binding pockets were shown as transparent volumes, whose surface color shows its relation to the two structures along the component: pink for the orange colored structure and blue for the blue colored structure. The pairwise distances (dashed lines in (a–c)) among the C_α atoms of three key residues (1: Q152, 2: R64 and 3′: R69′ in the other monomer, labeled with spheres in (a–c)) in the pockets were shown in (d). The distances are named as d_ij for the distances between the ith and jth residues in (d). The solid and dashed lines were for front and back pockets, respectively.