Simulation report

Technical information

General information

Name: Human smoothened receptor (apoform)

PDB id: 4QIN

Activation state: Inactive

Submitted by: Ainoleena Turku, Karolinska Institutet

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Chloride (156 mM), Sodium ion (145 mM)

Number of molecules:

Water: 14916

POPC: 160

Chloride: 42

Sodium ion: 39

Smoothened homolog: 1

Total number of atoms: 71969

Simulation details

Software and version: GROMACS, 2016.5

Forcefield and version: CHARMM, 36m

Time step : 2.0 fs

Delta : 0.2 ns

Replicates: 3

Accumulated simulation time: 0.6006 µs

Additonal parameters: Available at "Simulation protocol & starting files"



References

Kozielewicz P, Turku A, Bowin C-F, Petersen J, Valnohova J, Consuelo Alonso Cañizal M, Ono Y, Inoue A, Hoffmann C, Schulte G. 2020. Structural insight into small molecule action on Frizzleds. Nature communications 1 (11). doi: 10.1038/s41467-019-14149-3. (https://doi.org/10.1038/s41467-019-14149-3)


Simulation components

Receptor

PDB id: 4QIN
Smoothened homolog

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(39 molecules)

Na+


Chloride

Specific State ID: 5017

(42 molecules)

Cl-


POPC

Specific State ID: 5018

(160 molecules)


Water

Specific State ID: 5019

(14916 molecules)

H2O