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. 2018 Feb 5;8:2427. doi: 10.1038/s41598-018-20775-6

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© The Author(s) 2018

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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A comparison of the binding of stigmatellin, AC0-12 and myxothiazol to Ndi1, in relation to the UQ_I and UQ_II sites. (A) Close-up views of the overlap projection of the binding of stigmatellin (STG-1a: aqua; STG-1b: green), myxothiazol (blue) and AC0-12 (red) to Ndi1 (transparent gray). (B) A close-up view of the ubiquinone at the UQ_I (transparent pink) and UQ_II (transparent pale orange) sites, which were adapted by superimposing the Ndi1-ubiquinone complex structure (PDB code: 4G74) proposed by Feng et al.²⁹. The amino acid residues that form a space for the UQ_I and UQ_II sites at the si-face of FAD are shown in transparent yellow meshes. (C,D) The overlap projection of ubiquinone in UQ_I and UQ_II sites with stigmatellin at STG-1a site (C) and stigmatellin at STG-1b, AC0-12 and myxothiazol (D). (E) The predicted UQ_I site in ubiquinone reduction by Ndi1. The structures determined for the Ndi1-stigmatellin, Ndi1-ubiquinone (PDB code: 4G74)²⁹ and Ndi1-NAD⁺ complexes (PDB code: 4GAP)²⁸ are superposed. The ubiquinone molecule (magenta) in the UQ_I site and NAD⁺ molecule (yellow) are located on the si-face and re-face of the isoalloxazine ring of FAD (white), respectively. The head group of stigmatellin in both positions of STG-1a (transparent aqua) and STG-1b (transparent green), as well as the alkenyl chain of stigmatellin in the position of STG-1a overlaps with the UQ_I site.