Table 2.
Structural parameters of the selected TREM-1/ligands complexes.
| Protein | TREM-1 / Actin | TREM-1 / eCIRP1–110 | TREM-1 / HMGB1 | TREM-1 / Hsp70 | TREM-1 / PGRLYP1 | TREM-1 / APOA1 |
|---|---|---|---|---|---|---|
| pLDDT | 59.2 | 75.9 | 74 | 83.4 | 94.3 | 59.2 |
| pTM score | 0.337 | 0.547 | 0.393 | 0.766 | 0.908 | 0.337 |
| ipTM | 0.0939 | 0.231 | 0.206 | 0.387 | 0.872 | 0.0939 |
| MolProbity score | 1.33 | 1.99 | 1.82 | 1.62 | 1.48 | 2.06 |
| Clashscore | 3.29 | 9.59 | 4.4 | 6.53 | 3.6 | 7.68 |
| Poor rotamers | 1.91% | 0.53% | 0.70% | 1.11% | 1.22% | 6.98% |
| Favored rotamers | 94.99% | 97.33% | 94.41% | 96.66% | 95.93% | 84.13% |
| Bad bonds | 0% | 0% | 0% | 0% | 0% | 0% |
| Bad angles | 0.36% | 0.51% | 0.67% | 0.45% | 0.32% | 0.79% |
| Ramachandran’s most favored¹ | 93.6% | 88.2% | 82.1% | 93.4% | 89.3% | 98.1% |
| Ramachandran’s disallowed¹ | 0.2% | 0% | 0.4% | 0.3% | 0.8% | 0% |
APOA1 - Apolipoprotein A-I; eCIRP - extracellular cold-inducible RNA-binding protein; Hsp70–70 kDa heat shock protein; HMGB1 - high mobility group box 1 protein; dHMGB1 – disulfide HMGB1; rHMGB1 – reduced HMGB1; PGLYRP1 - peptidoglycan recognition protein 1; ¹Residues found in the most favored and disallowed regions of the Ramachandran plot, in analysis with PROCHECK.