Table 3B.
Molecular docking scores of ligands (napin and cruciferin) and bacterial receptor proteins (1xbp, 3fra, 3fyv, and 4urm).
| Complex name | Sol no | aElec | rElec | laElec | lrElec | HB | piS | catpiS | aliph | Transformation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1xbp and napin | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −2.182 0.785 −0.167 153.825 85.611 72.471 |
| 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −2.546 0.068 0.002 107.452 28.385 110.538 | |
| 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3.055 0.849 −1.166 90.032 169.446 145.327 | |
| 9 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2.831 0.483 −1.078 114.903 66.700 61.513 | |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −2.716 −0.099 −0.070 103.328 74.379 76.142 | |
| 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −0.435 −0.617 1.439 100.459 74.442 79.054 | |
| 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −0.432 0.132 −3.035 101.192 71.071 75.851 | |
| 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −0.446 0.219 −2.705 102.389 70.811 74.034 | |
| 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −1.959 −0.076 −2.320 100.384 71.509 77.724 | |
| 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2.622 −0.218 −1.907 109.921 69.589 72.565 | |
| 1xbp and procruciferin | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −1.479 −0.555 −0.584 157.666 116.809 83.178 |
| 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.050 −0.527 −0.712 157.651 121.770 178.506 | |
| 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.861 −0.884 −2.532 132.500 −12.579 49.529 | |
| 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −2.937 0.836 −2.558 120.442 27.038 99.815 | |
| 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.305 0.080 2.319 93.522 27.314 125.913 | |
| 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −2.781 −0.979 −1.829 124.149 −5.545 92.508 | |
| 9 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −0.348 −0.341 1.407 135.052 73.380 18.199 | |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −2.786 −0.160 −2.122 86.345 −2.855 45.882 | |
| 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.014 −0.912 2.859 36.535 187.629 −33.873 | |
| 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | −2.169 −0.881 2.534 136.756 46.109 89.104 | |
| 3FRA and napin | 3 | 0 | 0 | 0 | 3.65 | −1.16 | 0 | 0 | 0 | −0.374 0.333 −2.558 48.513 22.971 58.415 |
| 7 | 0 | 2.53 | 0 | 5.59 | −4.27 | 0 | −3 | 0 | 2.498 0.263 0.565 31.811 −9.349 22.582 | |
| 6 | −39.57 | 49.91 | −14.84 | 25.75 | −3.61 | −5 | −1.5 | 0 | 0.777 −0.920 0.031 31.240 −6.76720.236 | |
| 2 | −18 | 13.15 | −5.6 | 4.24 | 0 | 0 | 0 | 0 | −1.844 −0.378 2.308 33.992 13.213 72.834 | |
| 10 | 0 | 44.64 | 0 | 28.65 | −3.13 | −3 | 0 | 0 | −1.866 0.052 −1.199 54.995 6.205 39.585 | |
| 9 | −31.84 | 52.4 | −2.64 | 20 | −5.53 | −1.5 | 0 | 0 | 2.809 −0.276 −1.675 32.913 −6.274 20.409 | |
| 5 | −3.67 | 92.55 | −8.86 | 14.77 | −5.3 | −3.5 | 0 | 0 | −1.765 −0.023 −1.244 52.431 5.865 40.971 | |
| 1 | −4.3 | 12.91 | −3.53 | 27.28 | −4.66 | −3 | 0 | 0 | −1.910 −0.035 −1.076 55.277 9.872 38.750 | |
| 8 | 0 | 168.99 | −13.9 | 16.5 | −8.96 | −6 | −1.5 | 0 | 1.154 −0.855 0.068 30.797 −3.343 19.271 | |
| 4 | −18.94 | 63.43 | −5.72 | 13.39 | −7.83 | −8.5 | −0.5 | 0 | −2.319 −0.115 −2.030 42.600 −6.846 29.913 | |
| 3FRA and procruciferin | 7 | −63.76 | 76.16 | −26.94 | 7.65 | −2.6 | −0.5 | −4.5 | 0 | −2.395 −0.295 3.104 −40.270 5.564 75.524 |
| 5 | −47.32 | 155.69 | −20.65 | 12.73 | −7.49 | −1.5 | 0 | 0 | −2.400 1.033 1.077 61.649 63.589 28.921 | |
| 6 | −33.43 | 83.8 | −15.12 | 5.66 | −2.01 | −0.5 | −1.5 | 0 | −1.829 −1.362 −0.374 −21.860 23.311 19.302 | |
| 9 | −9.05 | 70.71 | −19.39 | 24.64 | −4.39 | −3.5 | −2 | 0 | 2.402 −0.332 −1.654 −27.722 −6.950 50.787 | |
| 1 | −77.85 | 44.59 | −31.15 | 25.54 | −3.36 | −3.5 | 0 | 0 | −1.451 1.285 −1.855 53.382 −39.770 50.677 | |
| 8 | −9.3 | 6.63 | −11.71 | 35.54 | −1.28 | −2 | 0 | 0 | −0.997 −0.228 0.402 67.781 63.930 47.546 | |
| 3 | −35.06 | 88.26 | −21.91 | 27.64 | −1.53 | −0.5 | 0 | 0 | 0.037 −0.982 2.915 −18.447 −36.805 −29.202 | |
| 2 | −97.95 | 166.22 | −19.3 | 37.74 | −2.73 | −1.5 | 0 | 0 | −1.708 −0.533 −1.055 −17.817 −34.684 8.139 | |
| 10 | 0 | 97.58 | −9.94 | 14.63 | −2.21 | 0 | −0.5 | 0 | −1.396 −0.553 0.583 50.656 74.284 19.120 | |
| 4 | −7.53 | 126.93 | −26.95 | 30.3 | −4.65 | −4.65 | −3 | 0 | 2.312 −0.378 −1.677 −26.461 −9.600 53.378 | |
| 3fyv and napin | 7 | −18.13 | 0 | −2.56 | 0 | −0.63 | 0 | 0 | 0 | 1.195018 0.111900 −0.404503 36.603848 13.070419 67.113762 |
| 10 | −4.79 | 57.17 | −8.34 | 26.33 | −0.92 | −3 | −1.5 | 0 | 1.419516 1.422478 −0.341556 48.927547 4.558572 42.616772 | |
| 8 | 0 | 113.12 | −2.71 | 24.28 | −3.99 | −1.5 | −0.5 | 0 | 0.897423 −0.512778 0.087532 38.153831 −4.305618 22.148920 | |
| 2 | −12.15 | 64.62 | −5.29 | 25.39 | −4.08 | −2.5 | 0 | 0 | 0.571090 −0.669658 −0.104022 34.059589 −7.079601 22.993988 | |
| 3 | 0 | 33.55 | −2.32 | 31.86 | −1.32 | 0 | 0 | 0 | 0.327455 1.276970 2.856120 54.459126 8.206043 44.482044 | |
| 9 | 0 | 38.48 | −2.61 | 14.07 | −1.43 | 0 | −0.5 | 0 | 2.365478 0.011664 1.090053 35.474125 −9.137678 22.458466 | |
| 6 | −4.16 | 0 | −7.4 | 3.81 | −4.35 | −3 | 0 | 0 | 0.186018 −0.592759 2.217820 21.126738 36.698421 53.015606 | |
| 5 | −73.96 | 26.78 | −27.29 | −27.29 | −4.61 | −1.5 | −1.5 | 0 | −1.635767 −0.367702 1.973211 6.267393 32.485970 42.305016 | |
| 1 | 0 | 0 | −2.41 | 0 | −10.39 | −3 | 0 | 0 | 0.183982 −0.287892 1.906260 25.036688 33.092117 58.026882 | |
| 4 | −5.03 | 0 | −8.11 | 0 | −8.82 | −1 | −0.5 | 0 | −0.185922 0.394067 −1.593941 26.694721 12.248711 70.375458 | |
| 3fyv and procrucifrerin | 3 | −98.07 | 83.04 | −17.98 | 9.03 | −8.49 | −0.5 | −3.5 | 0 | 0.882312 0.270622 0.452004 34.376209 16.761656 105.629204 |
| 1 | −61.41 | 84.22 | −22.21 | 5.66 | −2.95 | −1.5 | −3.5 | 0 | −2.408909 −0.310804 3.137617 −40.343742 3.093425 74.197830 | |
| 2 | −140.35 | 79.66 | −6.04 | 7.93 | −3.92 | 0 | −1.5 | 0 | −0.871412 0.289663 −1.703906 −3.532524 −71.564064 81.714600 | |
| 8 | −71.86 | 42.05 | −18.43 | 25.3 | −1.69 | −1.5 | −1.5 | −1.5 | −2.924418 −1.277309 −0.012886 −4.014475 −30.156733 16.353909 | |
| 7 | −19.67 | 5.26 | −2.47 | 4.59 | −2.47 | −0.5 | 0 | 0 | −1.000771 −0.166307 2.180230 29.872753 95.077187 34.847866 | |
| 10 | −4.48 | 2.47 | −16.22 | 1.67 | −0.83 | −1.5 | 0 | 0 | 1.584941 1.442978 1.329863 17.483091 −43.860760 60.712036 | |
| 5 | −44.84 | 84.56 | −22.3 | 40.69 | −4.93 | −2.5 | 0 | 0 | −2.497311 1.305315 −0.634158 63.377178 −31.635798 44.732738 | |
| 9 | −31.71 | 130.52 | −30.34 | 19.31 | −2.67 | −0.5 | −1.5 | 0 | −2.693943 0.193235 0.101170 114.073677 8.710386 87.306931 | |
| 6 | −68.99 | 58.52 | −39 | 11.46 | −12.24 | −5.5 | 0 | −1.5 | 0.541106 0.042602 −0.569371 98.065758 −28.758331 7.812671 | |
| 3 | 0 | 90.92 | −3.16 | 11.64 | −7.58 | −4.5 | −0.5 | −0.5 | −0.486131 1.271754 −2.446670 46.617748 −29.963055 47.164417 | |
| 4urm and napin | 7 | −98.45 | 64.66 | −54.86 | 8.7 | −2.99 | 0 | 0 | −0.5 | 1.868066 −0.092131 1.525814 3.637999 −3.130833 89.582695 |
| 6 | −21.61 | 5.28 | −8.68 | 9.4 | −1.67 | 0 | −1.5 | 0 | −1.460179 0.502492 1.252873 −0.179193 −0.899414 90.955017 | |
| 8 | −37.47 | 2.22 | −18.01 | 6.93 | −7.41 | −0.5 | −0.5 | 0 | −2.274868 −0.086826 1.442803 −1.433655 −8.620634 21.917574 | |
| 5 | 0 | 0 | −11.27 | 5.51 | −3.48 | 0 | 0 | 0 | 2.159986 0.164253 −1.314865 0.505913 −3.224665 87.916992 | |
| 2 | −17.01 | 0 | −2.35 | 0 | −0.59 | 0 | 0 | 0 | −1.886352 −0.360272 2.477731 −30.973713 −4.360527 86.722488 | |
| 10 | −3.7 | 0 | −23.82 | 0 | 0 | 0 | 0 | −0.5 | −2.866194 0.273189 −1.994032 −2.115814 0.507240 85.711090 | |
| 3 | 0 | 0 | 0 | 3.38 | −0.87 | 0 | 0 | 0 | −0.317704 −0.848188 −0.778242 1.825974 0.354532 101.007179 | |
| 9 | −77.7 | 42.28 | −23.21 | 15.08 | −2.23 | 0 | 0 | 0 | 1.982411 0.129197 −0.731296 3.800283 3.508109 88.668083 | |
| 1 | −26.53 | 96.95 | −11.3 | 33.03 | −0.43 | 0 | −1.5 | −1 | −2.776647 −0.022754 2.788598 −6.041031 −2.748431 83.736801 | |
| 4 | −13.84 | 65.53 | −22.31 | 18.81 | −3.28 | −3 | −2 | 0 | 2.470320 0.397040 −2.668524 6.743612 −16.430897 23.362900 | |
| 4urm and procruciferin | 10 | −36.17 | 5.34 | −14.5 | 0 | 0 | 0 | 0 | 0 | 1.135997 −0.824196 −0.303326 0.146988 1.550484 90.916000 |
| 6 | −22.1 | 14.31 | −4.85 | 8.27 | −1.27 | 0 | −0.5 | 0 | 0.572244 1.138489 1.520022 54.118980 70.514359 110.521210 | |
| 2 | 0 | 0 | 0 | 6.37 | −1.25 | −0.5 | 0 | −0.5 | 0.100003 1.048633 −0.000666 96.403412 −40.060814 111.336456 | |
| 4 | −65.72 | 98.02 | −36.28 | 28.24 | −2.67 | 0 | −1.5 | −3 | −2.418812 0.821444 −1.755734 −42.335209 −13.986760 148.038712 | |
| 5 | 0 | 29.32 | −3.1 | 8.75 | 0 | 0 | 0 | 0 | 2.891166 −0.650604 −1.210649 −9.728887 −14.524008 98.395508 | |
| 3 | 0 | 32.64 | 0 | 25.43 | 0 | 0 | 0 | 0 | −1.590922 0.173499 −0.392852 10.746419 5.179658 91.331253 | |
| 9 | −12.58 | 77.45 | −24.05 | 37.72 | −3.99 | 0 | 0 | 0 | −2.217826 −1.256601 −2.375825 −26.934299 46.748051 64.341164 | |
| 1 | −72.36 | 167.22 | −25.94 | 63.32 | −3.48 | 0 | 0 | −0.5 | −2.266007 0.966959 −2.883063 25.514585 −12.810349 162.878510 | |
| 8 | 0 | 52.53 | −2.58 | 11.68 | −2.33 | 0 | 0 | 0 | 1.868728 0.001705 −0.450134 102.784889 19.933956 61.477333 | |
| 7 | 0 | 0 | 0 | 0 | −4.04 | 0 | 0 | 0 | 0.937499 0.348988 1.225773 9.959099 −7.660954 132.986313 |
aElec, rElec, attractive and repulsive short-range Coulomb electrostatics; laElec, lrElec, attractive and repulsive long-range Coulomb electrostatics; HB, hydrogen and disulfide bonds; piS, PI-PI stacking; catpiS, cation-PI stacking; aliph, aliphatic interactions; Transformation, ligand transformation after refinement; Sol no, Solution number. 1XBP is the 50S ribosomal subunit from Deinococcus radiodurans, 3FRA is Staphylococcus aureus dihydrofolate reductase, 4URM is S. aureus gyrase B, and 3FYV is S. aureus dihydrofolate reductase. All the other sequences were retrieved from the GenBank database and are as follows (source species and sequence accession numbers are shown in parenthesis): Mabinlin-II (Capparis masaikai; P30233), Sesa1 (Arabidopsis thaliana; P15457), Napin-2 (Brassica napus; P01090), Sin a 1 (Sinapis alba; P15322), Napin-1A (B. napus; P24565), Ric c 3 (Ricinus communis; P01089), Ber e 1 (Bertholletia excelsa; P04403), Ric c 1 (R. communis; P01089), and Gm2S-1 (Glycine max; P19594). Bacterial receptor proteins were selected by efficient global search of relative receptor-ligand interactions (Andrusier et al., 2007; Barakat et al., 2016).