Structures in pdb format for the paper "How structural dynamics influence the substrate oxidation energetics in lytic polysaccharide monooxygenases"
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| Formato: | Recurso digital |
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Zenodo
2025
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| _version_ | 1866902160431644672 |
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| author | Hedegård, Erik |
| author_facet | Hedegård, Erik |
| contents | <ol> <li>QM/MM optimized structures for all intermediates and transition states (QM regions, full enzymes and Big-QM regions).</li> <li>Molecular dynamics movies of three example trajectories of the LPMO–substrate complex over 100 ns: lpmo-glc3_1.mp4 and lpmo-glc6_1.mp4 show examples of constructive binding for the substrates Glc3 and Glc6, respectively; lpmo-glc3_2.mp4 (Movie S1 in the paper) shows a trajectory involving a conformational change of the trimer, resulting in an unproductive binding mode.</li> <li><span>md_files.zip contains the initial structures for the Cu(I)-Glc3 and Cu(I)-Glc6 complex used to start the MD simulations, the Amber input files, and the custom force field file for Cu(I) and the coordinating NE2 of the terminal histidine.</span></li> </ol> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17102294 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Structures in pdb format for the paper "How structural dynamics influence the substrate oxidation energetics in lytic polysaccharide monooxygenases" Hedegård, Erik LPMO Molecular dynamics QM/MM <ol> <li>QM/MM optimized structures for all intermediates and transition states (QM regions, full enzymes and Big-QM regions).</li> <li>Molecular dynamics movies of three example trajectories of the LPMO–substrate complex over 100 ns: lpmo-glc3_1.mp4 and lpmo-glc6_1.mp4 show examples of constructive binding for the substrates Glc3 and Glc6, respectively; lpmo-glc3_2.mp4 (Movie S1 in the paper) shows a trajectory involving a conformational change of the trimer, resulting in an unproductive binding mode.</li> <li><span>md_files.zip contains the initial structures for the Cu(I)-Glc3 and Cu(I)-Glc6 complex used to start the MD simulations, the Amber input files, and the custom force field file for Cu(I) and the coordinating NE2 of the terminal histidine.</span></li> </ol> |
| title | Structures in pdb format for the paper "How structural dynamics influence the substrate oxidation energetics in lytic polysaccharide monooxygenases" |
| topic | LPMO Molecular dynamics QM/MM |
| url | https://doi.org/10.5281/zenodo.17102294 |