Fig. 3: The detailed interactions between 6L3-3P11K and the major RBDs. | Nature Communications

Fig. 3: The detailed interactions between 6L3-3P11K and the major RBDs.

From: Intranasal administration of broad-spectrum macrocyclic peptide inhibitor protects against SARS-CoV-2 Omicron variants

Fig. 3: The detailed interactions between 6L3-3P11K and the major RBDs.

The footprints of 6L3-3P11K on the RBD of SARS-CoV-2 PT (a) and Omicron BA.2.75 (e) are shown in green and mauve, respectively. The RBD protein is depicted in surface representation. b, f The hydrophobic interactions between 6L3-3P11K and RBDs. c, g The hydrogen bond interactions between 6L3-3P11K and RBDs. The RBD protein is depicted in cartoon representation, and the amino acids of RBD involved in the interaction with 6L3-3P11K are displayed as sticks and darkened in color. Hydrogen bonds are displayed as a red dashed line. d Comparison between structures of S/6L3-3P11K RBD (gray) and SARS-CoV-2 PT RBD (PDB: 6VXX, light blue). The F374-K378 loop of RBD in the S/6L3-3P11K complex exhibited a noteworthy conformational change. h Comparison between structures of BA.2.75 S/6L3-3P11K RBD (orange) and SARS-CoV-2 Omicron BA.2.75 RBD (PDB: 7YQU, light green). The F374-K378 loop in the two RBDs showed minimal conformational changes. Single-letter abbreviations for the amino acid residues are as follows: D, Asp; G, Gly; F, Phe; I, Ile; K, Lys; L, Leu; P, Pro; N, Asn; S, Ser; T, Thr; V, Val; and Y, Tyr.

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