Fig. 3: MD simulations show robust contacts between AlstR-C and V029-3547.

a Ribbon and surface representation of V029-3547:AlstR-C complex. V029-3547 is at the orthosteric pocket, located at the receptor’s extracellular site. Ligand is colored blue and represented in ball and stick format. Loop regions in contact with the compound are colored yellow (ECL1), green (ECL2), and purple (ECL3). The orange-colored surface shows the binding pocket of AlstR-C. b Protein-ligand interactions plot shows the contacts throughout the simulations. Stacked bar charts are normalized according to simulation time. Purple: hydrophobic interactions, green: hydrogen bonds, blue: water bridges, and pink: ionic interactions. c Detailed representation of interactions of active site residues and ligand atoms. Interactions that occur more than 15.0% of the simulation time, are shown. Lime color shows hydrophobic contacts, and blue illustrates the water bridges. Green is an indicator of π-π stacking interactions. d Illustration of the interactions and contacts throughout the simulation time. The top panel depicts the total number of contacts, while the bottom panel displays which residues interact with the ligand in each trajectory frame. A deeper shade of orange denotes specific residues that make more than one contact with the ligand. Source data are provided as a Source Data file.