Simulation report

Technical information

General information

Name: A2a adenosine receptor & cholesterol

PDB id: 3EML

Activation state: Inactive

Description: Classical unbiased (NVT ensemble) complex flexibility assay.

Submitted by: GPCR drug discovery group (Pompeu Fabra University)

System setup

Solvent type: TIP3P

Membrane type: Heterogeneous

Membrane composition: DSPC (5.3%), DPPC (14.2%), CHL1 (33.2%), DOPC (10.7%), SM18 (23.4%), SDPC (13.1%)

Ionic composition: Sodium ion (158 mM), Chloride (182 mM)

Number of molecules:

Water: 22908

Cholesterol: 112

W-203937: 79

Chloride: 75

Sodium ion: 65

DDPC: 48

SDPC: 44

DOPC: 36

DSPC: 18

Adenosine receptor A2a: 1

Total number of atoms: 112357

Simulation details

Software and version: ACEMD, 3203m

Forcefield and version: CHARMM, 36

Time step : 4.0 fs

Delta : 0.1 ns

Replicates: 1

Accumulated simulation time: 0.0997 µs



References

R. Guixà-González, J. L. Albasanz, I. Rodriguez-Espigares, M. Pastor, F. Sanz, M. Martí-Solano, M. Manna, H. Martinez-Seara, P. W. Hildebrand, M. Martín, J. Selent. 2017. Membrane cholesterol access into a G-protein-coupled receptor. Nature Communications 8. doi: doi:10.1038/ncomms14505. (http://www.nature.com/articles/ncomms14505)


Simulation components

Ligands

Orthosteric ligand(s)

Cholesterol

(112 molecules)


Receptor

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Mutations

No mutations found



Other molecules



DDPC

Specific State ID: 5024

(48 molecules)


DSPC

Specific State ID: 5025

(18 molecules)


SDPC

Specific State ID: 5026

(44 molecules)


W-203937

Specific State ID: 5027

(79 molecules)


Sodium ion

Specific State ID: 5016

(65 molecules)

Na+


Chloride

Specific State ID: 5017

(75 molecules)

Cl-


Water

Specific State ID: 5019

(22908 molecules)

H2O


Cholesterol (orthosteric lig.)

Specific State ID: 5022

(112 molecules)


DOPC

Specific State ID: 5023

(36 molecules)