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. Author manuscript; available in PMC: 2019 Mar 29.
Published in final edited form as: J Comput Aided Mol Des. 2018 May 8;32(6):671–685. doi: 10.1007/s10822-018-0120-3

Fig. 3.

Fig. 3

The first PC modes from Cartesian PCA of apo CDK8/CycC or CDK8/CycC-Ligand complexes using 100 ns trajectories. The breathing motion between N-lobe (cyan) and C-lobe (green) (a), breathing motion between CDK8 and Cyclin (yellow) (b), rotational motion between N-lobe and C-lobe (c), rotational motion between CDK8 and Cyclin (d), and loop motions (e) are indicated by gray arrows for DMG-In (Left) and DMG-Out (Right) conformations. The DMG-In PC modes use MD1 100–200 ns (a), MD3 0–100 ns (b), MD1 200–300 ns (c), MD5 0–100 ns (d), MD5 200–300 ns (e). The DMG-Out PC modes use MD11 100–200 ns (a), MD7 100–200 ns (b), MD11 300– 400 ns (c), MD8 100–200 ns (d), MD9 100–200 ns (e)