Simulation report
Technical information
General information
Name: Gpr34 receptor complex with ligand m1
PDB id: 8XBI
Description: -
Submitted by: Luying Chen, University of Tokyo
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Sodium ion (156 mM), Chloride (320 mM)
Number of molecules:
Water: 7474
POPC: 89
Chloride: 43
Sodium ion: 21
M1: 1
Probable G-protein coupled receptor 34: 1
Total number of atoms: 39497
Simulation details
Software and version: maestro, 2019-3
Forcefield and version: OPLS, OPLS3e
Time step : 2.0 fs
Delta : 0.1 ns
Replicates: 1
Accumulated simulation time: 1.0002 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Tamaki Izume, Ryo Kawahara, Akiharu Uwamizu, Luying Chen, Shun Yaginuma, Jumpei Omi, Hiroki Kawana, Fengjue Hou, Fumiya K. Sano, Tatsuki Tanaka, Kazuhiro Kobayashi, Hiroyuki H. Okamoto, Yoshiaki Kise, Tomohiko Ohwada, Junken Aoki, Wataru Shihoya, Osamu Nureki. 2024. Structural basis for lysophosphatidylserine recognition by GPR34. Nature Communications 15. doi: doi.org/10.1038/s41467-024-45046-z. (https://www.nature.com/articles/s41467-024-45046-z#Abs1)
GPCRmd publication page: 1506
Simulation components
Ligands
Receptor
Mutations
No mutations found
