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Simulation report

Technical information

General information

Name: Triple-mutant beta2 adrenergic receptor in complex with gs protein

PDB id: 3SN6

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: Sodium ion (161 mM), Chloride (148 mM)

Number of molecules:

Water: 35234

POPC: 255

Sodium ion: 102

Chloride: 94

LEVISOPRENALINE: 1

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short: 1

Total number of atoms: 156536

Simulation details

Software and version: GROMACS, 2019.3

Forcefield and version: CHARMM, 36m

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

Orthosteric ligand(s)

Levisoprenaline

(1 molecule)


Receptor

PDB id: 3SN6

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

Table of simulated mutations

(Mutations shown in blue at the viewer)

Residue ID Residue seq. position Generic num. From To
212 174 - L -
212 174 - T -


Other molecules



Water

Specific State ID: 5151

(35234 molecules)

H2O


Sodium ion

Specific State ID: 5153

(102 molecules)

Na+


LEVISOPRENALINE (orthosteric lig.)

Specific State ID: 5320

(1 molecule)


Chloride

Specific State ID: 5154

(94 molecules)

Cl-


POPC

Specific State ID: 5152

(255 molecules)


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