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. Author manuscript; available in PMC: 2017 Jul 31.
Published in final edited form as: J Mol Biol. 2016 May 30;428(15):2943–2964. doi: 10.1016/j.jmb.2016.05.024

Figure 4. Energy surface and encounter complexes.

Figure 4

(a) IRMSD from the native complex vs. the energy function obtained by docking histidine-containing phosphocarrier protein (HPr) to the N-terminal domain of Enzyme I (EIN). Clusters around the three lowest energy minima are indicated. (b) Native complex formed by EIN (gray surface) and HPr (shown as yellow cartoon). Centers of HPr structures in the encounter complex ensemble are shown as small spheres. Colors indicate classification as follows: Cluster 1, overlapping with the final complex, blue; Cluster 2, encounter complex within 20Å RMSD from the final complex, but not overlapping with it; Cluster 3, encounter complex around 30Å RMSD from the final complex. A number of low energy structures that do not belong to any of these clusters are shown in pink. (c) Same as b, but after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN.