Fig. 2: RM-A interacts with ScIleRS from multiple directions and forms extensive polar interactions and hydrophobic contacts with ScIleRS.

a Zoomed-in view of the binding site of the C1-10 triene acid segment of RM-A. The hydrogen bonds formed with water molecules (red spheres) are indicated as red dashed lines, and the polar interactions between RM-A and the residues of ScIleRS are described as black dashed lines. b–d Zoomed-in view of the binding sites of the C20-24 diene acid moiety (b), the hemisuccinate (c), and the butyl alkyl side chain (d) of RM-A. e Two-dimensional presentation of RM-A binding. The ligands RM-A and Ile-AMP and the residues forming polar interactions with RM-A are shown in ball-and-stick representations, and other residues within 4.5 Å of RM-A are shown in grey. The H-bonding structural water molecules (W) are shown in red spherical models. f C-terminal truncated ScIleRS or its variants at 1 μM or 3 μM were added to rabbit reticulocyte lysate to test their capability to rescue the protein translation inhibited by 200 nM RM-A. Almost all of the mutations, except W449A, strongly reduced the rescue capability of ScIleRS. All error bars represent standard deviations (SD) of three independent (n = 3) experiments, and the data are presented as mean values ± SD. Source data are provided as a Source Data file.