Table 2.
Values of the volume of the deep- or distal-binding pocket (DBP) (standard deviations in parentheses) in each conformer of AcrB, measured on the E. coli AcrBWT reference structures and on the molecular dynamics (MD) trajectories of S. Typhimurium AcrBWT and AcrBG288D (see Materials and Methods).
| System | Volume of DBP [Å3] | ||
|---|---|---|---|
| L-Conformer | T-Conformer | O-Conformer | |
| EcAcrBWT1 | 763 (86) | 2315 (76) | 1094 (76) |
| STmAcrBWT2 | 957 (93) | 1534 (163) | 991 (96) |
| STmAcrBG288D2 | 807 (78) | 1979 (72) | 1151 (64) |
1 calculated on experimental reference structures; 2 calculated on representatives of each of the 100 clusters extracted from the MD trajectories.