Table 1. MD and X-ray results for distances between binding sites of PDC109 and PhC.
| MD | Minimized | X-ray
|
|||
| domain | residue | protomer A | protomer A | protomer A | protomer B |
| PDC109/a | Y30 | 6.6 2.2 |
3.9 | 7.1 | 3.8 |
| Y54 | 6.9 2.1 |
4.3 | 12.4 | 3.8 | |
| W47 | 4.6 0.7 |
4.5 | 13.3 | 4.2 | |
| W58 | 4.6 0.7 |
4.7 | 16.7 | 4.4 | |
| Y60 | 8.1 3.1 |
6.8 | 14.0 | 10.6 | |
| Y75 | 5.9 2.0 |
5.3 | 9.3 | 3.9 | |
| PDC109/b | Y100 | 6.1 1.9 |
3.5 | 8.4 | 3.9 |
| W93 | 4.6 0.8 |
4.0 | 4.2 | 4.3 | |
| W106 | 4.5 0.6 |
5.0 | 4.9 | 4.2 | |
| Y108 | 8.8 2.6 |
7.3 | 3.5 | 10.4 | |
Distances are in Å and were determined by averaging through MD trajectories (protomer A) and from the crystal structure (protomers A and B, *PDB ID: 1h8p). Distances for tryptophans were calculated between the six-carbon ring centers of sidechain indoles and the PhC quaternary ammonium nitrogen. Distances for tyrosines were calculated between sidechain hydroxyl oxygens and the average position of three PhC phosphate oxygens. Average MD distances and standard deviations were calculated using the initial 230 ns trajectories because PhC started to detach from the binding pocket of PDC109/a at about 240 ns.