Table 1.
Features of proteins with substantial structural change in non-interacting regions and no/moderate change at interface
| PDB code | Cα RMSD | Normalized PB substitution score | ||||||
|---|---|---|---|---|---|---|---|---|
| Protein |
Bound |
Unbound |
IR* |
NIR_PBc* |
Difference |
IR* |
NIR_PBc* |
Difference |
| |
|
|
|
|
(NIR_PBc – IR) |
|
|
(NIR_PBc – IR) |
| PIP3 kinase (O) |
1HE8_r |
1E8Z |
0.49 |
8.45 |
7.96 |
1.25 |
-1 |
-2.25 |
| HISF protein (O) |
1GPW_r |
1THF |
0.68 |
8.10 |
7.42 |
1.68 |
-1.31 |
-2.99 |
| UCH-L3 (O) |
1XD3_r |
1UCH |
1.30 |
5.11 |
3.80 |
1.35 |
-1.05 |
-2.4 |
| Son of Sevenless (O) |
1BKD_r |
2II0 |
1.33 |
4.91 |
3.57 |
1.39 |
-0.82 |
-2.21 |
| TGF-beta (O) |
1KTZ_r |
1TGK |
0.66 |
4.41 |
3.75 |
2.1 |
-0.95 |
-3.05 |
| HPr kinase C-ter domain (E) |
1KKL_r |
1JB1 |
1.76 |
4.00 |
2.24 |
1.95 |
-0.98 |
-2.93 |
| Cystatin (E) |
1YVB_l |
1CEW |
0.63 |
3.85 |
3.21 |
2.43 |
-1.24 |
-3.67 |
| DH/PH domain of TRIO (O) |
2NZ8_r |
1NTY |
1.33 |
3.77 |
2.43 |
1.25 |
-0.78 |
-2.03 |
| Actin (O) |
2BTF_r |
1IJJ |
1.08 |
3.77 |
2.68 |
1.76 |
-0.81 |
-2.57 |
| Alpha-1-antitrypsin (E) |
1OPH_r |
1Q1P |
0.92 |
3.50 |
2.58 |
1.35 |
-1.39 |
-2.74 |
| TGFbeta receptor (O) |
1B6C_l |
1IAS |
1.17 |
3.14 |
1.96 |
1.28 |
-1.04 |
-2.32 |
| Vitamin D binding protein (O) |
1KXP_l |
1KW2 |
1.53 |
3.11 |
1.57 |
1.66 |
-0.77 |
-2.43 |
| TolB (O) |
2HQS_r |
1CRZ |
1.37 |
3.04 |
1.67 |
2 |
-0.81 |
-2.81 |
| RCC1 (O) |
1I2M_l |
1A12 |
0.40 |
3.00 |
2.60 |
2.43 |
-0.99 |
-3.42 |
| Sporulation response factor B (O) |
1F51_r |
1IXM |
0.78 |
2.70 |
1.92 |
1.1 |
-0.97 |
-2.07 |
| Ran GTPase (O) |
1A2K_l |
1QG4 |
0.33 |
2.57 |
2.24 |
2.56 |
-1.03 |
-3.59 |
| HEW lysozyme (A) |
1BVK_l |
3LZT |
0.31 |
2.57 |
2.25 |
2.86 |
-1.06 |
-3.92 |
| Transferrin receptor ectodomain (O) |
1DE4_l |
1CX8 |
0.94 |
2.51 |
1.57 |
1.04 |
-1.16 |
-2.2 |
| Anthrax toxin receptor (O) |
1T6B_l |
1SHU |
0.27 |
2.32 |
2.05 |
2.15 |
-0.75 |
-2.9 |
| Xylanase inhibitor (E) |
2B42_r |
1T6E |
0.33 |
2.25 |
1.91 |
2.06 |
-0.95 |
-3.01 |
| Fab (A) |
1E6J_r |
1E6O |
0.75 |
1.98 |
1.22 |
2.48 |
-0.73 |
-3.21 |
| Complement C3 (O) | 1GHQ_r | 1C3D | 0.21 | 1.58 | 1.36 | 1.92 | -0.69 | -2.61 |
*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 0.89 and 3.75, respectively. The normalized PB substitution score for IR and NIR_PBc values is 1.78 and -0.98, respectively.