Figure 3.

P2Y₆‐PGE₂‐G molecular dynamics‐refined docked model. PGE₂‐G as docked to P2Y₆ homology models, then the selected docked model was further refined with total of 1.5 μs of molecular dynamics. Lateral (A–B) and extracellular (C) views of the MD‐refined model of PGE₂‐G docked in the comparative model of the human P2Y₆ are shown. Hydrogen bonds are indicated as dashed yellow lines, and side chains of residues that are important to PGE₂‐G activity are shown in sticks. The seven transmembrane helices (TM) are numbered from N‐ to C‐terminal (I–VII). Plots of RMSD to the starting docked model throughout the MD simulation (D–E) and per‐residue RMSF after discarding the first 100 ns of the MD simulation (F) are given. To allow comparison between residues in the TM domain of different rhodopsin‐like GPCRs, residues are numbered according to the Ballesteros‐Weinstein numbering scheme ^[27] additionally to the position in the human P2Y₆.