Skip to main content

Advertisement

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 (Å) 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
  Average Verify3D-1D Normalized 3D Profile ProSA ERRAT
  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