Table 3 LOOPP server results for secondary structure matches of Pyrococcus furiosus , Neurospora crassa and Arabidopsis thaliana PA serine protease target sequence with known PDB structures
From: Modeling and structural analysis of PA clan serine proteases
PDB ID | Secondary structure | Â | Â | Score | Sequence identity (%) | Length (%) |
|---|---|---|---|---|---|---|
| Â | Helical structure (%) | Extended (%) | Loops /Other (%) | Â | Â | Â |
P. furiosus | ||||||
Target | 2.70 | 31.76 | 65.54 | - | - | - |
1GBI | 0.00 | 52.41 | 47.59 | 3.410 | 27.14 | 94.59 |
1SSX | 0.00 | 55.84 | 44.16 | 3.394 | 27.14 | 94.59 |
1GBM | 0.00 | 55.17 | 44.83 | 3.357 | 27.14 | 94.59 |
1BOQ | 0.00 | 52.41 | 47.59 | 3.343 | 27.14 | 94.59 |
1GBD | 0.00 | 55.17 | 44.83 | 3.292 | 27.14 | 94.59 |
N. crassa | ||||||
Target | 0.65 | 40.00 | 59.35 | - | - | - |
1VCW | 2.60 | 33.77 | 63.64 | 3.078 | 23.87 | 93.55 |
1L1J | 1.94 | 31.07 | 66.99 | 2.863 | 28.39 | 96.13 |
1TE0 | 2.74 | 32.19 | 65.07 | 2.742 | 24.66 | 87.74 |
1SOZ | 0.00 | 33.51 | 66.49 | 2.535 | 22.73 | 93.55 |
1SOT | 2.63 | 33.55 | 63.82 | 2.511 | 24.50 | 90.97 |
A. thaliana | ||||||
Target | 0.00 | 38.60 | 61.40 | - | - | - |
1L1J | 2.34 | 32.71 | 64.95 | 6.423 | 44.44 | 92.40 |
1VCM | 3.03 | 35.76 | 61.21 | 6.247 | 42.69 | 92.40 |
1TE0 | 3.03 | 33.33 | 63.64 | 6.134 | 42.11 | 92.40 |
1Y8T | 5.03 | 39.11 | 55.87 | 5.739 | 44.44 | 91.81 |
1SOZ | 0.51 | 34.52 | 64.97 | 5.315 | 42.69 | 92.40 |