Simulation report
Technical information
General information
Name: Ffa2_tug1375_gi1-tug1375-dock4cmtb
PDB id: 8J22
Activation state: Active
Description: Simulation aims to confirm the role of 4CMTB in FFA2 structural changes seen in FFA2/4CMTB complex by simulating 4CMTB docking pose to FFA2 from another structure. It produced NPT ensemble from 3 replicas of 1000 ns Langevin dynamics (T=310.15K, gamma=1ps-1) with semi-isotropic Berendsen barostat (P=1bar, tau=1ps) and 9A noncovalent cutoff.
Submitted by: Abdul-Akim Guseinov, University of Glasgow
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Number of molecules:
(2r,4r)-2-(2-chlorophenyl)-3-(4-(3,5-dimethylisoxazol-4-yl)benzoyl)thiazolidine-4-carboxylic acid: 1
(S)-4-CMTB: 1
Free fatty acid receptor 2: 1
Total number of atoms: 4863
Simulation details
Software and version: AMBER PMEMD.CUDA, 2020
Forcefield and version: ff19SB/lipid21/GAFF2, ff19SB/lipid21
Time step : 2.0 fs
Delta : 0.1 ns
Replicates: 3
Accumulated simulation time: 3.0 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Find a list of all simulations published in this paper: 1613
Simulation components
Ligands
(2r,4r)-2-(2-chlorophenyl)-3-(4-(3,5-dimethylisoxazol-4-yl)benzoyl)thiazolidine-4-carboxylic acid
(1 molecule)
(1 molecule)
Receptor
Mutations
Table of simulated mutations
(Mutations shown in blue at the viewer)
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|---|---|---|---|
| 291 | 291 | 8x61 | R | - |
| 291 | 291 | 8x61 | N | - |
| 291 | 291 | 8x61 | Q | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | S | - |
| 291 | 291 | 8x61 | S | - |
| 291 | 291 | 8x61 | L | - |
| 291 | 291 | 8x61 | L | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | R | - |
| 291 | 291 | 8x61 | R | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | K | - |
| 291 | 291 | 8x61 | D | - |
| 291 | 291 | 8x61 | T | - |
| 291 | 291 | 8x61 | A | - |
| 291 | 291 | 8x61 | E | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | T | - |
| 291 | 291 | 8x61 | N | - |
| 291 | 291 | 8x61 | E | - |
| 291 | 291 | 8x61 | D | - |
| 291 | 291 | 8x61 | R | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | V | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | Q | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | E | - |
| 291 | 291 | 8x61 | G | - |
| 291 | 291 | 8x61 | M | - |
| 291 | 291 | 8x61 | P | - |
| 291 | 291 | 8x61 | S | - |
| 291 | 291 | 8x61 | S | - |
| 291 | 291 | 8x61 | D | - |
| 291 | 291 | 8x61 | F | - |
| 291 | 291 | 8x61 | T | - |
| 291 | 291 | 8x61 | T | - |
Other molecules
(2r,4r)-2-(2-chlorophenyl)-3-(4-(3,5-dimethylisoxazol-4-yl)benzoyl)thiazolidine-4-carboxylic acid (allosteric lig.)
Specific State ID: 5402(1 molecule)
