Table 1. Kd, Bij, and the Contributions of Binding Interactions, Bij(b), and Nonbinding Interactions, Bij, to Bij for Three Protein Complexes (PDB codes 6LYZ, 1OTR, 1UUG) for the Insertion/Removal Method (“ins/rem”) and the Subvolume Method (“subvol”)a.
lysozyme | method | Kd [μM] | B22 [nm3] | B22(b) [nm3] | B22(u) [nm3] |
---|---|---|---|---|---|
ins/rem | 5191 ± 63 | –77 ± 4 | –160 ± 2 | 83 ± 4 | |
subvol | 5188 ± 68 | –78 ± 4 | –160 ± 2 | 82 ± 3 |
Ubi/CUE | method | Kd [μM] | B23 [nm3] | B23(b) [nm3] | B23(u) [nm3] |
---|---|---|---|---|---|
ins/rem | 153 ± 1 | –5444 ± 37 | –5435 ± 37 | –9 ± 3 | |
subvol | 153 ± 1 | –5455 ± 39 | –5444 ± 38 | –11 ± 3 |
UDG/Ugi | method | Kd [μM] | B23 [nm3] | B23(b) [nm3] | B23(u)[nm3] |
---|---|---|---|---|---|
ins/rem | 0.25 ± 0.002 | –3 332 000 ± 27 000 | –3 332 000 ± 27 000 | –94 ± 5 | |
subvol | 0.25 ± 0.002 | –3 308 000 ± 27 000 | –3 308 000 ± 27 000 | –81 ± 7 |
Errors are standard errors of the mean.