Simulation report
Technical information
General information
Name: Dopamine receptor 1 in complex with gs protein
PDB id: 7JVP
Activation state: Active
Submitted by: Nagarajan Vaidehi, Beckman Research Institute of the City of Hop
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Chloride (164 mM), Potassium-39 (151 mM)
Number of molecules:
Water: 49383
POPC: 349
Chloride: 146
Potassium-39: 134
1h-3-benzazepine-7,8-diol, 6-chloro-2,3,4,5-tetrahydro-3-methyl-1-(3-methylphenyl)-, (1r)-: 1
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short: 1
Total number of atoms: 210687
Simulation details
Software and version: GROMACS, 2019.3
Forcefield and version: CHARMM, CHARMM36
Time step : 2.0 fs
Delta : 0.2 ns
Replicates: 1
Accumulated simulation time: 1.0002 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Manbir Sandhu, Aaron Cho, Ning Ma, Elizaveta Mukhaleva, Yoon Namkung, Sangbae Lee, Soumadwip Ghosh, John H. Lee, David E. Gloriam, Stéphane A. Laporte, M. Madan Babu, Nagarajan Vaidehi. 2022. Dynamic spatiotemporal determinants modulate GPCR:G protein coupling selectivity and promiscuity. Nature Communications. doi: 10.1038/s41467-022-34055-5. (https://www.nature.com/articles/s41467-022-34055-5)
GPCRmd publication page: 1494
Simulation components
Ligands
1h-3-benzazepine-7,8-diol, 6-chloro-2,3,4,5-tetrahydro-3-methyl-1-(3-methylphenyl)-, (1r)-
(1 molecule)
Receptor
Mutations
Table of simulated mutations
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|
Other molecules
1h-3-benzazepine-7,8-diol, 6-chloro-2,3,4,5-tetrahydro-3-methyl-1-(3-methylphenyl)-, (1r)- (orthosteric lig.)
Specific State ID: 5313(1 molecule)
