Supplementary Data for "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase"

This dataset contains atomic coordinates of the molecular dynamics simulations described in "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase" by M. Alfonso-Prieto, I. Cuxart, G. Potocki-Véronèse, I. André and C. Rovira, published in ACS Catalysis (https://doi.org/10.1021/acscatal.3c00451). Further details on the setup of the simulations can be found in the Supplementary Information of the article. If you use this dataset, please cite this zenodo upload (https://doi.org/10.5281/zenodo.7704778), as well as the the original journal article (https://doi.org/10.1021/acscatal.3c00451). This dataset is organized in the following folders: <strong>Snapshots_Figures_Main_Text.zip</strong>, that contains a README.txt file and: <strong>- Figure_3</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP in complex with 3 different disaccharide molecules, Man-b-(1,4)-GlcNAc, Man-b-(1,4)-Glc and Man-b-(1,4)-Man. <strong>- Figure_4</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP at the three minima observed along the reaction coordinate corresponding to phosphorolysis of the disaccharide Man-b-(1,4)-GlcNAc: Michaelis complex (MC), transition state (TS) and product (P) complex. Files in this dataset are in PDB format. For all structures, the solvation box (water and ions) has been stripped to reduce file size. See README.txt inside Snapshots_Figures_Main_Text.zip for more information.本数据集包含M. Alfonso-Prieto、I. Cuxart、G. Potocki-Véronèse、I. André与C. Rovira发表于《ACS催化》（ACS Catalysis）的论文《肠道细菌甘露糖苷磷酸化酶降解N-聚糖的底物辅助机制》中所述分子动力学模拟（molecular dynamics simulations）的原子坐标（atomic coordinates），论文DOI为https://doi.org/10.1021/acscatal.3c00451。该模拟的搭建细节可参见该论文的补充材料。若使用本数据集，请同时引用本Zenodo上传资源（DOI：https://doi.org/10.5281/zenodo.7704778）与原始期刊论文（DOI：https://doi.org/10.1021/acscatal.3c00451）。 本数据集的组织形式如下：<strong>Snapshots_Figures_Main_Text.zip</strong>，该压缩包内含README.txt文件，以及以下子内容：<strong>- Figure_3</strong>：包含肠道细菌甘露糖苷磷酸化酶（UhgbMP）六聚体形式与3种不同二糖分子结合的代表性结构（原子坐标），三种二糖分别为Man-β-(1,4)-GlcNAc、Man-β-(1,4)-Glc及Man-β-(1,4)-Man。<strong>- Figure_4</strong>：包含肠道细菌甘露糖苷磷酸化酶（UhgbMP）六聚体形式在二糖Man-β-(1,4)-GlcNAc磷酸解反应路径上三个极小值点处的代表性结构（原子坐标），分别为米氏复合物（Michaelis complex, MC）、过渡态（transition state, TS）与产物复合物（product complex, P）。 本数据集的所有文件均采用PDB格式（Protein Data Bank format）。为减小文件体积，所有结构均已移除溶剂化盒（水与离子）。更多详细信息请参见Snapshots_Figures_Main_Text.zip压缩包内的README.txt文件。