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. 2020 Oct 12;10:16986. doi: 10.1038/s41598-020-74099-5

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Conformational diversity of the M^pro active site. The projection of the first two principal components (PC1 and PC2) is shown. The contribution ratios of first two principal components (PC1 and PC2) were 36.1% and 12.9%, respectively. The conformations of the active site, corresponding to the cross mark and (a)–(c) in the projection, are shown: the cross mark and (a)–(c) are the crystal structure (PDB ID: 6LU7) and simulation structures of indinavir-bound M^pro, saquinavir-bound M^pro, and lopinavir-bound M^pro systems, respectively. The five regions of the active site, (1) residues 24–27, (2) 41–54, (3) 140–145, (4) 163–168 and 172, and (5) 187–192, are coloured in red, blue, yellow, green, and magenta, respectively. The representative conformations for the active site of apo-M^pro system are shown in Supplementary Fig. J3. The Apo chain A and Apo chain B correspond to the trajectories of the active sites of the chain A and the chain B of the apo-M^pro system, respectively.