Simulation report
Technical information
General information
Name: Frizzled-6 in complex wih minigs/i (apoform)
PDB id: HOMO
Submitted by: Schulte lab, Karolinska Institutet
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Sodium ion, Water, Chloride
Number of molecules:
Water: 10000
POPC: 300
Chloride: 131
Sodium ion: 121
Smothened agonist: 1
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short: 1
Frizzled-6: 1
Total number of atoms: 183402
Simulation details
Software and version: GROMACS, 2019.2
Forcefield and version: CHARMM36, GAFF2, CHARMM36, GAFF2
Time step : 2.0 fs
Delta : 0.3 ns
Replicates: 3
Accumulated simulation time: 0.5463 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Ainoleena Turku; Hannes Schihada; Pawel Kozielewicz; Carl-Fredrik Bowin; Gunnar Schulte. 2021. Residue 6.43 defines receptor function in class F GPCRs. Nature communications 12 (1). doi: 10.1038/s41467-021-24004-z. (https://doi.org/10.1038/s41467-021-24004-z)
GPCRmd publication page: 1473
Simulation components
Receptor
Mutations
Table of simulated mutations
(Mutations shown in blue at the viewer)
281
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|---|---|---|---|
| 49 | 49 | - | G | D |
| 50 | 50 | - | E | N |
| 64 | 64 | - | V | - |
| 64 | 64 | - | N | - |
| 65 | 65 | - | F | - |
| 65 | 65 | - | N | - |
| 67 | 67 | - | E | S |
| 80 | 80 | - | D | - |
