Simulation report

Technical information

General information

Name: P2y purinoceptor 12 in complex with methylthio-adenosine diphosphate

PDB id: 4PXZ.A

Activation state: Intermediate

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 (240 mM), Sodium ion (156 mM)

Number of molecules:

Water: 13202

POPC: 157

Chloride: 57

Sodium ion: 37

Methylthio-adenosine diphosphate: 1

P2Y purinoceptor 12: 1

Total number of atoms: 65814

Simulation details

Software and version: ACEMD, GPUGRID

Forcefield and version: CHARMM, 36m Feb 2016

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)

Methylthio-adenosine diphosphate

(1 molecule)


Receptor

PDB id: 4PXZ.A
P2Y purinoceptor 12

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Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(37 molecules)

Na+


Methylthio-adenosine diphosphate (orthosteric lig.)

Specific State ID: 5056

(1 molecule)


POPC

Specific State ID: 5018

(157 molecules)


Water

Specific State ID: 5019

(13202 molecules)

H2O


Chloride

Specific State ID: 5017

(57 molecules)

Cl-