Published April 12, 2025
| Version v2
Dataset
Open
Conformational Signatures of Preassembled and Active Complexes of 5-HT7 with the Gs Protein
- 1. Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
- 2. Chemoinformatics and Protein Modelling, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- 1. Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
- 2. Chemoinformatics and Protein Modelling, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
Description
Initial topology, parameter and coordinates files of the Molecular dynamics (MD) simulations of 5-HT7 receptor. Three systems were simulated and analysed:
| System | System | State | Type |
| 1 | 5-CT:5-HT7:Gs active complex | active | refined model of 7XTC |
| 2 | GDP:5-HT7:Gs preassembled complex | Inactive | Model |
| 3 | 5-HT7 apo | Inactive | Model |
We used ACEMD3 (v3.5.1) as a molecular engine, CHARMM36 as force field. Each replicas of 500 ns (dcd files) were upload and save with the following naming scheme: system_<system_num>_replica_<replica_num>.dcd. Water molecules, ions, and membrane atoms (POPC: phosphatidylcholine) atoms were removed from the original trajectories and topology before the upload (dry_topology.pdb). The initial topology and CHARMM parameters (version july 2020) are stored in the toppar subfolder. The MD simulation of system 1 have been deposited into the GPCRmd database under access codes 2370.
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