Simulation report
Technical information
General information
Name: T360a v2rpp/b-arr1 complex + fab30
PDB id: 4JQI
Submitted by: Tomasz Stepniewski, IMIM
System setup
Solvent type: Implicit
Membrane type: Homogeneous
Ionic composition: Chloride (156 mM), Sodium ion (165 mM)
Number of molecules:
Water: 43319
Sodium ion: 129
Chloride: 122
Fab30: 1
Beta-arrestin-1: 1
Vasopressin V2 receptor: 1
Total number of atoms: 139773
Simulation details
Software and version: ACEMD3, GPUGRID
Forcefield and version: CHARMM, c36 Jul 2020
Time step : 4.0 fs
Delta : 1.0 ns
Replicates: 5
Accumulated simulation time: 10.0 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Mithu Baidya; Madhu Chaturvedi; Hemlata Dwivedi-Agnihotri; Ashutosh Ranjan; Dominic Devost; Yoon Namkung; Tomasz Maciej Stepniewski; Shubhi Pandey; Minakshi Baruah; Bhanupriya Panigrahi; Parishmita Sarma; Manish K. Yadav; Jagannath Maharana; Ramanuj Banerjee; Kouki Kawakami; Asuka Inoue; Jana Selent; Stéphane Laporte; Terence E. Hébert and Arun K. Shukla. None. Allosteric modulation of GPCR-induced β-arrestin trafficking and signaling by a synthetic intrabody. . doi: 10.1038/s41467-022-32386-x.
GPCRmd publication page: 1486
Simulation components
Ligands
Receptor
Mutations
Table of simulated mutations
1068
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|
