Fig. 6.
The conformational transition of ADK. (A) The evolution of χ angles along the progression of ADK trajectories from closed (Left) and open (Right) states toward similar terminal intermediates (Middle). (B) The coupling of χ1 and χ2. The conformations of intermediate crystal structures are shown on the χ1, χ2 domain angle space alongside dots at respective χ1, χ2, color-coded corresponding to C. Trajectories are plotted starting from closed-state ADK (Left) and open-state ADK (Right): entire structure involved in targeting (blue), AMP-lid domain excluded from targeting (red), and ATP-lid domain excluded from targeting (green). (C) Deviations (rmsd) between the trajectory intermediate states and respective intermediate crystal structures: semiclosed apo state (PDB ID: 2RH5) vs. the fully targeted trajectory (blue); complex with ATP analog AMPPCF2P (PDB ID: 1DVR) vs. the ATP-lid-directed trajectory (orange); and complex with AMP (PDB ID: 2AK3) vs. the AMP-lid-directed trajectory (green).