Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein
Table 4
Validation report for TLR2-ECD, TLR2-TIR, and MyD88-TIR homology models.
(a) Validation by SAVES server
Ramachandran plot (PROCHECK)
TLR2-ECD
TLR2-TIR
MyD88-TIR
Residue (%)
Residue (%)
Residue (%)
Most favored regions
66.7
78.7
73.2
Additionally allowed regions
30.0
20.6
24.4
Generously allowed regions
1.8
0.0
1.6
Disallowed regions
1.6
0.7
0.8
Verify3D score
95.37
97.28
87.6
ERRAT
61.059
86.364
86.325
PROVE (mean Z-score)
1.609
1.48
1.63
(b) Stereochemical quality of homology models by ProQ, ModFOLD, and MetaMQAP server
TLR2-ECD
TLR2-TIR
MyD88-TIR
ProQ (LG/MX)
7.062/0.432
6.401/0.772
7.067/0.847
ModFOLD (Q/P)
0.6326/0.0065
0.7473/0.00038
0.5787/0.0022
MetaMQAP (GDT/RMSD)
68.93/2.137
78.767/1.523
72.628/2.319
ProQ-LG: >1.5 fairly good; >2.5 very good; >4 extremely good. ProQ-MX: >0.1 fairly good; >0.5 very good; >0.8 extremely good. ModFOLD-Q: >0.5 medium confidence; >0.75 high confidence. ModFOLD-P: <0.05 medium confidence; <0.01 high confidence. MetaMQAP-GDT/RMSD: an ideal model has a GDT score over 59 and an RMSD around 2.0 Å.
