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. 2025 Aug 4;11(8):1670–1680. doi: 10.1038/s41477-025-02056-z

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© The Author(s) 2025

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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Fig. 3 — a, A cartoon representation highlighting movement in M6b and the M6b-7 loop of the bundle domain, as seen when going from the fully occluded conformational state (LAX3 2-NOA) to the inward semi-occluded conformational state (LAX3 IAA) and the inward open conformational state (LAX3 apo). b, Changes observed in the arms region of LAX3, including unwinding of M5b, when transitioning from the fully occluded state (2-NOA) to the inward semi-occluded state (IAA). For both a and b, M3 and M8 of the scaffold domain is shown in grey. c, The polar (θ) and unwrapped azimuthal (φ) angle (addressed in Extended Data Fig. 9) of IAA within the binding site used for clustering of the ligand into three distinct orientation clusters (cluster 1 in blue, cluster 2 in orange and cluster 3 in yellow). The remaining data points (grey) were unassigned. d, A close-up view of the representative (centroid) IAA poses for each of the three clusters assigned in c. e, The r.m.s.d. of IAA, with the background colour indicating the assigned cluster group for each simulation frame.