Figure 4.

Example of the tight superposition of similar ligands upon APF superposition of their binding sites: thiamine diphosphate in the binding sites of pyruvate dehydrogenase (1rp7, magenta) and pyruvate decarboxylase (1pvd, green). The resulting RMSD for thiamine ligand in this example is only 0.52A. At the same time even superimposable segments of the receptors’ secondary structure (transparent ribbons) experience much larger displacements. Sequence identity between the two proteins is 19.2%