Table 2.
Summary of representative models from the largest clusters by using any two cross-links as docking restraints. The solvent accessible area (SASA) of two most protected regions in IL-7, as indicated by HDX kinetics, are calculated for each docking model and for the unbound-state IL-7 in Pymol.
| Crosslink-based Restraints | Size of Largest Cluster | Model Category | SASA of Peptide in IL-7, Å | Matching with HDX (Y/N) | Compared to X-ray Structure, r.m.s.d, Å | ||||
|---|---|---|---|---|---|---|---|---|---|
| 19VSIDQL24 | 83VSEGTTIL90 | ||||||||
| Bound IL-7 in Models | Unbound IL-7 | Bound IL-7 in Models | Unbound IL-7 | ||||||
| 1_2 | 10 | Type 3 | 230 | 230 | 268 | 319 | N | 12.3 | |
| 1_3 | 26 | Type 1 | 133 | 220 | Y | 1.7 | |||
| 1_4 | 22 | Type 2 | 230 | 247 | N | 11.0 | |||
| 1_5 | 11 | Type 1 | 141 | 211 | Y | 1.4 | |||
| 2_3 | 25 | Type 1 | 158 | 213 | Y | 1.9 | |||
| 2_4 | 10 | Type 2 | 230 | 269 | N | 10.9 | |||
| 2_5 | 12 | Type 1 | 137 | 209 | Y | 1.5 | |||
| 3_4 | 15 | Type 1 | 142 | 214 | Y | 1.7 | |||
| 3_5 | 62 | Type 1 | 160 | 201 | Y | 1.7 | |||
| 4_5 | 4_5.1 | 13 | Type 1 | 127 | 213 | Y | 1.3 | ||
| 4_5.2 | 13 | Type 2 | 230 | 253 | N | 10.9 | |||