Table 5 Structural validation of the modeled PA proteases from Plasmodium falciparum , Pyrococcus furiosus, Neurospora crassa and Arabidopsis thaliana
From: Modeling and structural analysis of PA clan serine proteases
Structural model | All atom clashscore (No/1000 atoms) | Rotamer outliers (%) | RMSD of bond Length (Ã…) | RMSD of bond angle (Degree) |
|---|---|---|---|---|
X-ray structure (1L1J) | 4.33 | 7.49 | 0.029 | 2.74 |
Homology model of P. falciparum protease | 1.86 | 5.26 | 0.030 | 3.14 |
X-ray structure (1GBI) | 10.14 | 3.53 | 0.019 | 3.25 |
Threading model of P. furiosus protease | 15.00 | 2.63 | 0.019 | 3.21 |
X-ray structure (1VCW) | 3.23 | 4.58 | 0.024 | 3.91 |
Threading model of N. crassa protease | 5.38 | 8.47 | 0.020 | 3.37 |
X-ray structure (1L1J) | 4.33 | 7.49 | 0.029 | 2.74 |
Threading model of A. thaliana protease | 11.50 | 8.79 | 0.018 | 3.31 |
| Â | Average Verify3D-1D | Normalized 3D Profile | ProSA | ERRAT |
| Â | score | score (log 2 (Verify3D/L 2 ) | Z-score | quality Factor (%) |
X-ray structure (1L1J) | 0.46 | -10.95 | -8.43 | 79.4 |
Homology model of P. falciparum protease | 0.22 | -9.28 | -3.24 | 61.8 |
X-ray structure (1GBI) | 0.48 | -8.93 | -6.73 | 81.6 |
Threading model of P. furiosus protease | 0.19 | -9.52 | -3.27 | 71.2 |
X-ray structure (1VCW) | 0.38 | -12.80 | -7.73 | 80.6 |
Threading model of N. crassa protease | 0.24 | -9.32 | -3.81 | 52.6 |
X-ray structure (1L1J) | 0.46 | -10.95 | -8.43 | 79.4 |
Threading model of A. thaliana protease | 0.27 | -9.33 | -4.75 | 87.6 |