Table 2.
Proteins with substantial structural change in non-interacting regions and interfacial regions
| PDB code | Cα RMSD | Differences from global RMSD | Normalized PB substitution score | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Protein |
Bound |
Unbound |
IR* |
NIR_PBc* |
Global RMSD |
IR* – Global RMSD |
NIR_PBc* – Global RMSD |
IR* |
NIR_PBc* |
| Arf1 GTPase (O) |
1R8S_r |
1HUR |
5.19 |
5.42 |
3.02 |
2.17 |
2.40 |
0.79 |
-0.67 |
| Ras GTPase (O) |
1BKD_l |
1CTQ |
4.39 |
4.43 |
2.21 |
2.18 |
2.22 |
0.63 |
-1.82 |
| CDK2 kinase (E) |
1FQ1_l |
1B39 |
4.39 |
4.26 |
2.04 |
2.35 |
2.22 |
1.31 |
-1 |
| FC fragment of human IgG 1 (A) |
1E4K_r |
2DTQ |
3.17 |
3.77 |
2.18 |
0.99 |
1.59 |
0.95 |
-0.99 |
| Ran GTPase (O) |
1I2M_r |
1QG4 |
3.27 |
3.51 |
1.91 |
1.36 |
1.60 |
0.58 |
-0.8 |
| Cystein protease (E) |
1PXV_r |
1X9Y |
3.99 |
3.47 |
1.48 |
2.51 |
1.99 |
1.2 |
-1.04 |
| Rab21 GTPase (O) |
2OT3_l |
1YZU |
4.65 |
3.30 |
1.71 |
2.94 |
1.59 |
0.1 |
-0.6 |
| CDC42 GTPase (O) |
1GRN_r |
1A4R |
2.66 |
2.97 |
1 |
1.66 |
1.97 |
1.31 |
-0.96 |
| Rac GTPase (O) |
2NZ8_l |
1MH1 |
3.87 |
2.68 |
1.17 |
2.70 |
1.51 |
-0.03 |
-1.18 |
| Actin (O) |
1ATN_r |
1IJJ |
6.09 |
2.58 |
1.54 |
4.55 |
1.04 |
0.97 |
-0.59 |
| Rac GTPase (O) |
1I4D_l |
1MH1 |
2.31 |
2.52 |
0.81 |
1.50 |
1.71 |
1.15 |
-0.65 |
| Glycoprotein IB-alpha (E) | 1M10_l | 1MOZ | 3.95 | 2.12 | 0.89 | 3.06 | 1.23 | 0.91 | -0.95 |
*The abbreviations used are: IR - Interface regions, NIR_PBc – Non-interacting regions with PB change, l – ligand (smaller of the two proteins in the complex), r – receptor (bigger of the two proteins in the complex), E – enzyme-inhibitor complex, A – Antigen-antibody complex, O – Other complexes.
The proteins are listed in decreasing order of average Cα RMSD of NIR_PBc values. The average Cα RMSD of IR and NIR_PBc is 3.99 and 3.42, respectively. The average difference in RMSD values for IR and NIR_PBc from global RMSD are 2.33 and 1.75, respectively. The normalized PB substitution score for IR and NIR_PBc values is 1.737 and −0.95, respectively.