Simulation report

Technical information

General information

Name: C-x-c chemokine receptor type 4 in complex with it1t

PDB id: 3ODU.A

Activation state: Inactive

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

Submitted by: GPCRmd community

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Chloride (207 mM), Sodium ion (157 mM)

Number of molecules:

Water: 13418

POPC: 173

Chloride: 50

Sodium ion: 38

It1t: 1

C-X-C chemokine receptor type 4: 1

Total number of atoms: 68347

Simulation details

Software and version: ACEMD, GPUGRID

Forcefield and version: CHARMM, 36m Feb

Time step : 4.0 fs

Delta : 0.2 ns

Replicates: 3

Accumulated simulation time: 1.5 µs

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



References

Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, et al.. 2020. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature methods 17 (8). doi: 10.1038/s41592-020-0884-y. (http://doi.org/10.1038/s41592-020-0884-y)


Simulation components

Ligands

Orthosteric ligand(s)

It1t

(1 molecule)


Receptor

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Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(38 molecules)

Na+


Chloride

Specific State ID: 5017

(50 molecules)

Cl-


POPC

Specific State ID: 5018

(173 molecules)


It1t (orthosteric lig.)

Specific State ID: 5067

(1 molecule)


Water

Specific State ID: 5019

(13418 molecules)

H2O