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. 2022 Jul 5;13:3872. doi: 10.1038/s41467-022-31443-9

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© The Author(s) 2022

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a Overview of CD1a-DDM-CO3 ternary structure shows the ligand orientation in the cleft of CD1a (lilac). DDM (magenta) fully occupies A’ and F’ pockets and does not significantly protrude through the F’ portal of CD1a. b Relative position of the ligands in the cleft of CD1a bound to sulfatide (yellow) and DDM (magenta) in CD1a-CO3 ternary structures is shown. c Comparison of CD1a backbone in CO3-CD1a-sulfatide complex (light grey) and CO3-CD1a-DDM complex (lilac) shows that deoxymycobactic acid moiety of DDM (magenta) expands the F’ pocket of CD1a by conformational changes of hydrophobic residues within the cleft of CD1a. d DDM-induced F’ pocket expansion is associated with a 3 Å displacement of the CD1a-α1 helix towards the FRγ region (green) of CO3 leading to a formation of an additional hydrogen bond (blue line) between CD1a^His86 and the main chain of CO3γ.