Molecular Dynamics Trajectories for the D3 receptor (D3R) complexes bound with a GαOβγ heterotrimer and 1) FOB02-04A bitopic agonist; 2) pramipexole.

Molecular Dynamics Data for publication "Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket". Sandra Arroyo-Urea, Antonina L. Nazarova, Ángela Carrión-Antolí et al., Nat. Comm., revision (2024). https://doi.org/10.21203/rs.3.rs-3433207/v1

This directory includes the PDB (Protein Data Bank) format file detailing the topology and the XTC (eXtended Trajectory) format file outlining the trajectories for two distinct complexes: 1) the FOB02-04A-bound structure of D3 receptor (D3R) complexes in association with a GαOβγ heterotrimer, and 2) the pramipexole-bound structures of D3R complexes also coupled to a GαOβγ heterotrimer. The data is organized in a strided trajectory with a timestep of 0.5 nanoseconds per frame. To reapply periodic boundary conditions, users can employ the standard periodic boundary condition commands available in Visual Molecular Dynamics (VMD) package.

The MD trajectory data for this study was acquired as well as uploaded by Antonina L. Nazarova.