Free cookie consent management tool by TermsFeed GPCRmd
× Due to a recent server update, this page will be slow for the next 1-2 hours. We apologize for any inconvenience this may cause.

Simulation report

Technical information

General information

Name: Uman smoothened receptor (apoform)

PDB id: 6OT0

Activation state: Active

Submitted by: Schulte lab, Karolinska Institutet

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Chloride (572 mM), Sodium ion (550 mM)

Number of molecules:

Water: 10000

POPC: 301

Chloride: 103

Sodium ion: 99

Smothened agonist: 1

Smoothened homolog: 1

Total number of atoms: 156399

Simulation details

Software and version: GROMACS, 2019.2

Forcefield and version: CHARMM36, GAFF2, CHARMM36, GAFF2

Time step : 2.0 fs

Delta : 0.3 ns

Replicates: 4

Accumulated simulation time: 1.2507000000000001 µs

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

References

Ainoleena Turku; Hannes Schihada; Pawel Kozielewicz; Carl-Fredrik Bowin; Gunnar Schulte. 2021. Residue 6.43 defines receptor function in class F GPCRs. Nature communications 12 (1). doi: 10.1038/s41467-021-24004-z. (https://doi.org/10.1038/s41467-021-24004-z)



GPCRmd publication page: 1473

Simulation components

Receptor

PDB id: 6OT0
Smoothened homolog

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

Table of simulated mutations

Residue ID Residue seq. position Generic num. From To


Other molecules



Water

Specific State ID: 5019

(10000 molecules)

H2O


Chloride

Specific State ID: 5017

(103 molecules)

Cl-


Smothened agonist

Specific State ID: 5167

(1 molecule)


POPC

Specific State ID: 5018

(301 molecules)


Sodium ion

Specific State ID: 5016

(99 molecules)

Na+


PARTNER SERVERS

GPCRdb

GPCR-ModSim

GPCRM

NMRlipids

HomolWat

Hybrid MM/CG Webserver

CONTACT & LINKS

Documentation

Cite us

Privacy policy

Cookies policy

Disclaimer

Terms & Conditions

SUPPORTED BY

ERNEST (COST Action CA18133)

GLISTEN (COST Action CM1207)

GPCRForum