Table 4.
Comparison of the disulfide bond configurations in proteins that have very similar X-ray and NMR structures.
| Protein | X-Ray | NMR | Structural Similarity | |||||||||
| PDB | resolution | disulfides | configuration | DSE, kJ.mol-1 | PDB | models | disulfides | configuration1 | DSE, kJ.mol-1 | RMSD3 | MaxSub4 | |
| thioredoxin | 2tir | 2 | 32–35 | +/-RHHook | 1xoa | 20 | 32–35 | -RHHook (15) | 0.93 | 0.93 | ||
| +/-RHHook (5) | ||||||||||||
| ferredoxin II | 1fxd | 1.7 | 18–42 | +/-RHSpiral | 1f2g | 15 | 18–42 | -RHHook (5) | 0.96 | 0.93 | ||
| +/-LHStaple (5) | ||||||||||||
| +/-RHSpiral (5) | ||||||||||||
| ribonulcease A | 1kf5 | 1.1 | 26–84 | -LHSpiral | 7.1 | 2aas | 32 | 26–84 | -LHSpiral (16) | 12.6 (11.8–13.3)2 | 1.1 | 0.92 |
| -RHHook (13) | ||||||||||||
| -RHSpiral (3) | ||||||||||||
| 40–95 | -LHSpiral | 4.3 | 40–95 | -LHSpiral (32) | 4.1 (3.4–4.8) | |||||||
| 58–110 | -LHSpiral | 10.7 | 58–110 | -LHSpiral (30) | 11.4 (11.1–11.7) | |||||||
| -RHHook (2) | ||||||||||||
| 65–72 | -LHHook | 65–72 | -RHHook (32) | |||||||||
| ovomucoid | 2ovo | 1.5 | 8–38 | -LHSpiral | 6.1 | 1tur | 12 | 8–38 | -LHSpiral (12) | 23.0 (20.6–25.4) | 2.04 | 0.89 |
| 16–35 | +/-LHSpiral | 16–35 | -LHSpiral (11) | |||||||||
| -RHSpiral (1) | ||||||||||||
| 24–56 | -RHHook | 6.4 | 24–56 | -RHHook (6) | 11.1 (10.4–11.8) | |||||||
| -LHHook (3) | ||||||||||||
| -LHStaple (3) | ||||||||||||
| tendamistat | 1hoe | 2 | 11–27 | -/+RHHook | 2ait | 9 | 11–27 | +/-LHStaple (9) | 3.57 | 0.87 | ||
| 45–73 | -LHSpiral | 45–73 | -RHHook (3) | |||||||||
| -RHSpiral (2) | ||||||||||||
| -LHSpiral (1) | ||||||||||||
| +/-LHStaple (1) | ||||||||||||
| +/-RHHook (1) | ||||||||||||
| -LHHook (1) | ||||||||||||
| erabutoxin B | 3ebx | 1.4 | 3–24 | -LHSpiral | 2.8 | 1fra | 14 | 3–24 | -LHSpiral (11) | 23.2 (13.7–32.7) | 1.42 | 0.87 |
| -LHHook (2) | ||||||||||||
| -RHHook (1) | ||||||||||||
| 17–41 | -LHSpiral | 17–41 | -RHHook (11) | |||||||||
| -LHHook (1) | ||||||||||||
| -/+LHHook (1) | ||||||||||||
| +/-RHHook | ||||||||||||
| 43–54 | -RHSpiral | 43–54 | -LHSpiral (6) | |||||||||
| -RHSpiral (5) | ||||||||||||
| -RHHook (2) | ||||||||||||
| -RHStaple (1) | ||||||||||||
| 55–60 | +RHSpiral | 10.4 | 55–60 | +RHSpiral (9) | 38.1 (35.5–40.6) | |||||||
| +/-RHSpiral (4) | ||||||||||||
| +LHSpiral (1) | ||||||||||||
| lipid transfer protein | 1mzl | 1.9 | 4–52 | -LHSpiral | 1afh | 15 | 4–52 | +/-RHSpiral (10) | 1.67 | 0.84 | ||
| -RHHook (3) | ||||||||||||
| -RHSpiral (2) | ||||||||||||
| 14–29 | +/-RHHook | 14–29 | +/-LHStaple (5) | |||||||||
| +/-RHHook (3) | ||||||||||||
| -LHStaple (3) | ||||||||||||
| -/+LHHook (2) | ||||||||||||
| -LHHook (2) | ||||||||||||
| 30–75 | -LHSpiral | 4.4 | 30–75 | -LHSpiral (12) | 23.9 (22.4–25.3) | |||||||
| -LHHook (2) | ||||||||||||
| -RHHook (1) | ||||||||||||
| 50–89 | +/-LHSpiral | 50–89 | +/-LHHook (6) | |||||||||
| -LHSpiral (5) | ||||||||||||
| +/-LHSpiral (3) | ||||||||||||
| +/-RHHook (1) | ||||||||||||
| β-lactoglobulin | 1bsy | 2.2 | 66–160 | -RHSpiral | 9.3 | 1dv9 | 21 | 66–160 | -RHSpiral (4) | 39.9 (29.5–50.3) | 2.36 | 0.83 |
| -LHSpiral (3) | ||||||||||||
| +/-LHSpiral (3) | ||||||||||||
| -/+LHHook (3) | ||||||||||||
| +/-RHStaple (2) | ||||||||||||
| -LHHook (2) | ||||||||||||
| +/-RHSpiral (1) | ||||||||||||
| +/-RHHook (1) | ||||||||||||
| +/-LHStaple (1) | ||||||||||||
| -/+RHHook (1) | ||||||||||||
| 106–119 | -RHStaple | 15.8 | 106–119 | -RHStaple (12) | 18.6 (17.1–20.2) | |||||||
| -LHStaple (8) | ||||||||||||
| -LHHook (1) | ||||||||||||
| ribonulcease T1 | 4rnt | 2.2 | 2–10 | -LHHook | 15.3 | 1ygw | 34 | 2–10 | -LHHook (16) | 26.6 (26.5–26.8) | 1.82 | 0.82 |
| +/-RHStaple (10) | ||||||||||||
| -/+RHHook (4) | ||||||||||||
| -RHStaple (3) | ||||||||||||
| -RHHook (1) | ||||||||||||
| 6–103 | -RHStaple | 11.7 | 6–103 | -RHStaple (28) | 28.9 (25.8–32.1) | |||||||
| -RHHook (6) | ||||||||||||
| β2-microglobulin | 1lds | 1.8 | 25–80 | -LHStaple | 1jnj | 20 | 25–80 | -LHSpiral (10) | 3.46 | 0.77 | ||
| -RHSpiral (7) | ||||||||||||
| -RHHook (3) | ||||||||||||
1 Numbers in brackets are the number of disulfides with that configuration.
2 The mean dihedral strain energy (DSE) and 95% confidence intervals.
3 The root-mean square deviations (RMSD) value was calculated between all Cα atoms of the X-ray structure and the first NMR model [16].
4 MaxSub is a measure of structural similarity of the X-ray and NMR structures [16]. A score of 1.0 means that all Cα atoms are matched between the X-ray and NMR structures, while a score towards zero indicates very different structures. All the structures listed in the table have only small-scale differences (MaxSub values from 0.77 to 0.93).