Table 5.
Molecular docking of epitopes with HLA.
| MHC Class I | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| No. | Protein ID, name | Epitope | Global Energy | ||||||||
| HLA-A*0101 (PDB: 6AT9) | HLA-A*0201 (PDB: 3UTQ) | HLA-B*1501 (PDB: 1XR8) | HLA-B*3501 (PDB: 1ZSD) | HLA-B*3901 (PDB: 4O2E) | HLA-B*4403 (PDB: 1SYS) | HLA-B*5301 (PDB: 1A1M) | HLA-B*5801 (PDB: 5IM7) | Average | |||
| 1 | WP_041033700.1 D-alanyl-D-alanine carboxypeptidase/endopeptidase | TPFGAGWSW | -54.89 | -18.06 | -34.65 | -42.60 | -13.15 | -43.74 | -38.83 | -33.18 | -34.89 |
| LEDRLVETL | -41.35 | -22.48 | -43.79 | -24.36 | -35.34 | -16.97 | -38.40 | -23.62 | -30.79 | ||
| 2 | WP_141960268.1 Phospholipase C, phosphocholine-specific | FTIPLPGDR | -46.08 | -24.55 | -15.99 | -24.14 | -6.21 | -15.41 | -33.75 | -23.74 | -23.73 |
| 3 | WP_048321499.1 spore coat U domain-containing protein | SSNVNFPLY | -56.28 | -23.22 | -32.65 | -9.88 | -19.00 | -36.62 | -37.51 | -30.24 | -30.68 |
| 4 | WP_033636744.1 TonB-dependent receptor | QTYGAKIAR | -43.86 | -4.69 | -22.38 | -19.36 | -15.90 | -25.60 | -18.49 | -26.75 | -22.13 |
| SEYVWNYEL | -40.96 | -17.05 | -33.96 | -25.68 | -8.14 | -15.25 | -42.89 | -39.22 | -27.89 | ||
| YQFLKGWEL | -49.03 | -18.24 | -15.98 | -8.29 | -15.5 | -25.71 | -47.98 | -35.74 | -27.06 | ||
| MHC Class II | |||||||||||
| Global Energy | |||||||||||
| No. | Protein ID, name | Epitope | HLA-DRB1*0101 (PDB: 2FSE) | HLA-DRB1*0301 (PDB: 1A6A) | HLA-DRB1*0401 (PDB: 2SEB) | HLA-DRB1*1501 (PDB: 1BX2) | HLA-DRB3*0101 (PDB: 2Q6W) | HLA-DRB3*0202 (PDB: 3C5J) | HLA-DRB5*0101 (PDB: 1H15) | Average | |
| 1 | WP_041033700.1 D-alanyl-D-alanine carboxypeptidase/endopeptidase | WLLPAILALAGCSSS | -89.74 | -79.65 | -74.83 | -68.81 | -65.01 | -43.20 | -72.52 | -70.54 | |
| PGARAGAPGRVSFYP | -74.58 | -62.83 | -62.02 | -62.94 | -41.19 | -30.71 | -64.83 | -57.01 | |||
| LAVTFLKVSNNGYGE | -66.12 | -73.03 | -51.81 | -54.69 | -36.28 | -30.34 | -61.55 | -53.40 | |||
| PLAFAIISNNYLVPG | -72.3 | -57.61 | -55.05 | -62.76 | -58.5 | -47.77 | -89.92 | -63.42 | |||
| 2 | WP_084827239.1 patatin-like phospholipase family protein | SGASAGAIAALLVGL | -58.55 | -72.12 | -64.58 | -75.20 | -59.65 | -41.55 | -64.48 | -62.30 | |
| 3 | WP_141960268.1 Phospholipase C. phosphocholine-specific | RQYRAASIQVGNPAR | -61.17 | -55.80 | -47.44 | -47.05 | -13.96 | -30.96 | -69.12 | -46.50 | |
| EKRFQVHEPNISAWR | -38.13 | -38.77 | -45.12 | -8.34 | -16.93 | -24.41 | -27.34 | -28.43 | |||
| 4 | WP_048321499.1 spore coat U domain-containing protein | SLNLLSLILISSNVN | -88.21 | -56.66 | -52.15 | -68.53 | -29.65 | -50.10 | -89.29 | -62.08 | |
| LSLILISSNVNFPLY | -93.62 | -65.33 | -50.97 | -82.72 | -16.16 | -46.28 | -45.35 | -57.20 | |||
| 5 | WP_033636744.1 TonB-dependent receptor | NVGANAFLSGTRPRL | -65.95 | -52.33 | -55.04 | -61.88 | -20.96 | -31.18 | -58.32 | -49.38 | |
| NAFLSGTRPRLNLSL | -74.06 | -48.43 | -59.42 | -37.86 | -35.10 | -31.70 | -35.66 | -46.03 | |||
| TDFNINRPTAYNIQY | -42.87 | -44.67 | -49.32 | -32.67 | -13.94 | -34.32 | -43.83 | -37.37 | |||
| ADSRLHGLAGLRYFH | -62.54 | -47.66 | -53.30 | -61.08 | -24.56 | -25.95 | -58.13 | -47.60 | |||
| RWDFELFGNLGLLKT | -45.56 | -55.26 | -56.56 | -51.49 | -16.14 | -32.27 | -63.07 | -45.76 | |||
| ARAPAYTANMGAKYQ | -45.59 | -44.37 | -51.96 | -44.44 | -22.36 | -29.58 | -34.58 | -38.98 | |||
| AKYQFLKGWELSSNV | -54.33 | -61.70 | -39.90 | -59.14 | -18.93 | -25.68 | -38.05 | -42.53 | |||
3D structures were generated by the PEP-FOLD3 server. The docking was performed using PatchDock online tool and the results were refined by FireDock online server.