Fig. 6: Representative structures and water occupancy from MD simulations.
From: Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels
a Close-up view of the blocker binding sites after the MD simulations of GluK2NpTx8 (blue), GluK2PhTx74 (green), GluK2KukoA (violet), and GluK2SPM (orange), with blocker molecules (yellow) and residues involved in their binding shown in stick representation. The red dashed lines show the hydrogen bonds between the blockers and the binding site residues, the blue dashed lines show the hydrophobic contacts between the blockers and the hydrophobic side chains of the protein residues. Only two (A and C) of four subunits are shown, with the front and back subunits (B and D) removed for clarity. For GluK2KukoA, two representative structures (Pose 1 and Pose 2) from different parts of simulation are shown. b Similar views as in a, but with water molecules shown as red and white sticks.
