Simulation report
Technical information
General information
Name: Gpr34 receptor complex with ligand s3e-noamine-lysops
PDB id: 8XBG
Description: -
Submitted by: Luying Chen, University of Tokyo
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Sodium ion (157 mM), Chloride (321 mM)
Number of molecules:
Water: 7443
POPC: 92
Chloride: 43
Sodium ion: 21
S3e-noamine-lysops: 1
Probable G-protein coupled receptor 34: 1
Total number of atoms: 39812
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
