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Simulation report

Technical information

General information

Name: Htr2a in complex with mini-galpha-q protein

PDB id: 6WHA

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: Potassium-39 (151 mM), Chloride (150 mM)

Number of molecules:

Water: 47714

POPC: 353

Potassium-39: 130

Chloride: 129

Nboh-2c-cn: 1

5-hydroxytryptamine receptor 2A: 1

Total number of atoms: 204711

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

Orthosteric ligand(s)

Nboh-2c-cn

(1 molecule)


Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



POPC

Specific State ID: 5152

(353 molecules)


Potassium-39

Specific State ID: 5315

(130 molecules)

K


Nboh-2c-cn (orthosteric lig.)

Specific State ID: 5314

(1 molecule)


Water

Specific State ID: 5151

(47714 molecules)

H2O


Chloride

Specific State ID: 5154

(129 molecules)

Cl-


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