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. Author manuscript; available in PMC: 2020 Jun 16.
Published in final edited form as: Nat Chem Biol. 2019 Dec 16;16(3):310–317. doi: 10.1038/s41589-019-0423-2

Figure 6. Modeling of relative placement of antibiotics and tRNA substrates in the PTC active site.

Figure 6.

a. Overlay of the bound CHL molecule and the predicted position of the lysine amino-acid (Lys) on the A-site tRNA (A76 of both A-site and P-site tRNA shown; adapted based on PDB 1VY445 and amino-acid residues modeled). Lys is likely to clash with CHL (PDB 4V7T43), while the glycine (Gly) moiety can be properly accommodated without a direct steric clash. b. Overlay of the LZD (PDB 3CPW44) with CHL and tRNAs bound to the A site and P site of the ribosome. LZD is likely to clash with Gly on the A-site tRNA. c. Overlay of hygromycin A (HYG) with CHL and LZD (PDB 5DOY24). HYG is likely to clash directly with the A76 of A-site tRNA.