Fig. 7: Identification of an alternative pocket in the THF riboswitch.
From: Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN
In the upper panel, cartoon representation and molecular surface of the center of the most populated RNA cluster found in the SHAMAN simulation initiated from a holo-like conformation (PDB 4lvx). The THF riboswitch presents two binding pockets (dashed circles), one in a three-way junction (HB4 ligand bound between helical domains P2, P3 and P4, right side) and the other in a pseudoknot (HB4 ligand bound in PK region, left side). The experimental ligands in PDB 4lvx are superimposed by aligning the coordinates to the RNA cluster center. Our protocol detected a low free-energy SHAMAP in the middle of the THF riboswitch between helix P2 and P3 (surfaces surrounded by orange circle, colored as defined in Tab. S7 and S8),. In the lower panel, the light gray and light orange tables report the details of the SHAMAPs that identified the two experimental and the alternative binding sites, respectively.
