Simulation report

Technical information

General information

Name: Inactive fzd6 bound to smoothened agonist

PDB id: HOMO

Submitted by: Ainoleena Turku, Karolinska Institutet

System setup

Solvent type: TIP3P

Membrane type: Heterogeneous

Membrane composition: POPC

Ionic composition: Chloride (185 mM), Sodium ion (147 mM)

Number of molecules:

Water: 15897

POPC: 176

Chloride: 53

Sodium ion: 42

Protonated smoothened agonist: 1

Frizzled-6: 1

Total number of atoms: 77153

Simulation details

Software and version: GROMACS, 2016.5

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"


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

Ligands

Orthosteric ligand(s)

Protonated smoothened agonist

(1 molecule)


Receptor

PDB id: HOMO
Frizzled-6

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Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(42 molecules)

Na+


Chloride

Specific State ID: 5017

(53 molecules)

Cl-


Protonated smoothened agonist (orthosteric lig.)

Specific State ID: 5138

(1 molecule)


Water

Specific State ID: 5019

(15897 molecules)

H2O


POPC

Specific State ID: 5018

(176 molecules)