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Simulation report

Technical information

General information

Name: Human a2a adenosine receptor t4l chimera in complex with zothaebawxwvid-hxefrtelsa-n

PDB id: 5WF6

Activation state: Active

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: Sodium ion (157 mM), Chloride (182 mM)

Number of molecules:

Water: 26584

POPC: 224

Chloride: 87

Sodium ion: 75

Unii-8l3oaj1r5a: 1

Adenosine receptor A2a: 1

Total number of atoms: 115092

Simulation details

Software and version: ACEMD3, GPUGRID

Forcefield and version: CHARMM, c36 Jul 2020

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

Aranda-Garcia, David and Stepniewski, Tomasz Maciej and Torrens-Fontanals, Mariona and Garcia-Recio, Adrian and Lopez-Balastegui, Marta and Medel-Lacruz, Brian and Morales-Pastor, Adrian and Peralta-Garcia, Alejandro and Dieguez-Eceolaza, Miguel and Sotillo-Nunez, David and Ding, Tianyi and Drabek, Matthaus and Jacquemard, Celien and Jakowiecki, Jakub and Jespers, Willem and Jimenez-Roses, Mireia and Jun-Yu-Lim, Victor and Nicoli, Alessandro and Orzel, Urszula and Shahraki, Aida and Tiemann, Johanna K. S. and Ledesma-Martin, Vicente and Nerin-Fonz, Francho and Suarez-Dou, Sergio and Canal, Oriol and Pandy-Szekeres, Gaspar and Mao, Jiafei and Gloriam, David E. and Kellenberger, Esther and Latek, Dorota and Guixa-Gonzalez, Ramon and Gutierrez-de-Teran, Hugo and Tikhonova, Irina G. and Hildebrand, Peter W. and Filizola, Marta and Babu, M. Madan and Di Pizio, Antonella and Filipek, Slawomir and Kolb, Peter and Cordomi, Arnau and Giorgino, Toni and Marti-Solano, Maria and Selent, Jana. 2025. Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways. Nature Communications 16 (1). doi: 10.1038/s41467-025-57034-y. (http://dx.doi.org/10.1038/s41467-025-57034-y)



Find a list of all simulations published in this paper: GPCRmd publication id 1535

Simulation components

Ligands

Orthosteric ligand(s)

Unii-8l3oaj1r5a

(1 molecule)


Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Water

Specific State ID: 5151

(26584 molecules)

H2O


POPC

Specific State ID: 5152

(224 molecules)


Sodium ion

Specific State ID: 5153

(75 molecules)

Na+


Chloride

Specific State ID: 5154

(87 molecules)

Cl-


Unii-8l3oaj1r5a (orthosteric lig.)

Specific State ID: 5199

(1 molecule)


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