TABLE 2.
Summary of PDBeFOLD (45) superposition of structures found to be most similar to PmC11 in the PBD based on DaliLite (46)
The results are ordered in terms of structural homology (QH), where %SSEPC-X is the percentage of the SSEs in the PmC11 that can be identified in the target X (where X = caspase-7 (47), legumain (3), gingipain (48), and TcdB-CPD (49); % SSEX-PC is the percentage of SSEs in X (as above) that can be identified in PmC11 (as above); % sequence ID is the percentage sequence identity after structural alignment; Nalign is the number of matched residues; and r.m.s. deviation the root mean squared deviation on the Cα positions of the matched residues.
| Enzyme | Family | PDB code | QH | Z-score | %SSEPC-X | %SSEX-PC | % Seq. ID | Nalign | RMSD (Å) | NStrands |
|---|---|---|---|---|---|---|---|---|---|---|
| PmC11 | C11 | 3UWS | 1.00 | 33.4 | 100 | 100 | 100 | 352 | 0.00 | 9 |
| Caspase-7 | C14A | 4HQ0 | 0.16 | 4.3 | 38 | 79 | 14 | 162 | 3.27 | 6 |
| Legumain | C13 | 4AW9 | 0.13 | 5.5 | 31 | 53 | 13 | 161 | 2.05 | 6 |
| TcdB-CPD | C80 | 3PEE | 0.10 | 4.9 | 28 | 50 | 12 | 138 | 3.18 | 9 |
| Gingipain | C25 | 4TKX | 0.07 | 5.4 | 28 | 27 | 12 | 153 | 2.97 | 10 |