Fig. 4. Illustration of the conformational selection mechanism in apo form of the PDZ domain.

The apo form comprises an open ligand-welcoming (a) and a closed ligand-obstructing state (b). The surface views of the two states of the PDZ2 of the apo form, with state 1 (a) and state 2 (b) are shown with a transparent ribbon representation and the important sidechains of Lys38 and Lys72 (as sticks). The position of the RA-GEF2 peptide is visualized with a violet cylinder. The access to the binding groove is obstructed in PDZ2 apo state 2 by sidechains of residues Lys38 and Lys72 (b), which indicates the presence of a conformational selection mechanism upon ligand binding.