Simulation report

Technical information

General information

Name: Mu-type opioid receptor bound to oliceridine

PDB id: 5C1M

Activation state: Active

Description: Simulations generated using adaptive sampling. A set of simulations covering activation have been concatenated.

Submitted by: Marta Filizola, Icahn School of Medicine at Mout Sinai

System setup

Solvent type: TIP3P

Membrane type: Heterogeneous

Membrane composition: CHL1 (9.9%), POPC (90.1%)

Ionic composition: Sodium ion, Chloride

Number of molecules:

POPC: 137

Chloride: 41

Sodium ion: 27

Cholesterol: 15

Oliceridine: 1

Mu-type opioid receptor: 1

Total number of atoms: 24334

Simulation details

Software and version: ACEMD, 5.0.6

Forcefield and version: CHARMM, May 2015

Time step : 1.0 fs

Delta : 0.1 ns

Replicates: 1

Accumulated simulation time: 1.18 µs

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


Simulation protocol & starting files


References

Abhijeet Kapoor, Gerard Martinez-Rosell, Davide Provasi, Gianni de Fabritiis & Marta Filizola. 2017. Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity. Scientific reports 7 (1). doi: 10.1038/s41598-017-11483-8. (https://www.nature.com/articles/s41598-017-11483-8)


Simulation components

Ligands

Orthosteric ligand(s)

Oliceridine

(1 molecule)


Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

Table of simulated mutations

(Mutations shown in blue at the viewer)

Residue Generic num. From To
264 - M A
265 - L M


Other molecules



Sodium ion

Specific State ID: 5016

(27 molecules)

Na+


Chloride

Specific State ID: 5017

(41 molecules)

Cl-


POPC

Specific State ID: 5018

(137 molecules)


Oliceridine (orthosteric lig.)

Specific State ID: 5128

(1 molecule)


Cholesterol

Specific State ID: 5022

(15 molecules)