Table 1.
List of protein-RNA complexes used in the present study
| Complex | Organism | PDB code | RMSD (Å) | Sequence identity (%) | Binding site residues | |
|---|---|---|---|---|---|---|
| Protein (%) | RNA (%) | |||||
| Elongation Factor TU | E. coli | 1OB2:A | 1.4 | 71 | 7.63 | 22.37 |
| T. aquaticus | 1OB5:A | 9.14 | 20.78 | |||
| Leucyl-tRNA synthetase | E. coli | 4ARC:A | 1-2: 1.9 | 1-2: 45 | 4.09 | 25.29 |
| T. thermophilus | 2BTE:A | 1–3: 2.5 | 1–3: 27 | 3.08 | 22.89 | |
| P. horikoshii | 1WZ2:A | 2–3: 1.6 | 2–3: 29 | 3.21 | 18.18 | |
| Retinoic acid inducible protein I | A. platyrhynchos | 4A36:A | 2.6 | 59 | 4.14 | 28.95 |
| H. sapiens | 3TMI:A | 3.17 | 42.86 | |||
| Glutamyl-tRNA synthetase | T. maritima | 3AKZ:A | 2.3 | 41 | 9.65 | 33.78 |
| T. thermophilus | 1N78:A | 9.19 | 30.67 | |||
| Aspartyl-tRNA synthetase | E. coli | 1IL2:A | 1-2: 2.1 | 1-2: 49 | 7.12 | 32.00 |
| T. thermophilus | 1EFW:A | 1–3: 2.2 | 1–3: 28 | 3.97 | 20.55 | |
| S. cerevisiae | 1ASY:A | 2–3: 2.3 | 2–3: 30 | 8.57 | 26.67 | |
| Signal recognition particle | H. sapiens | 1MFQ:C | 1-2: 2.7 | 1-2: 36 | 9.30 | 6.25 |
| M. jannaschii | 2V3C:C | 1–3: 5.4 | 1–3: 32 | 5.79 | 18.48 | |
| S. solfataricus | 1QZW:A | 2–3: 1.29 | 2–3: 48 | 2.50 | 11.70 | |
| ATP dependent RNA helicase | H. sapiens | 3G0H:A | 1.1 | 51 | 5.19 | 100.00 |
| S. cerevisiae | 3PEY:A | 5.57 | 83.33 | |||
| Tyrosyl-tRNA synthetase | S. cerevisiae | 2DLC:X | 1-2: 1.7 | 1-2: 35 | 2.79 | 5.26 |
| M. jannaschii | 1J1U:A | 1–3: 2.7 | 1–3: 26 | 4.58 | 6.49 | |
| T. thermophilus | 1H3E:A | 2–3: 2.2 | 2–3: 27 | 4.63 | 16.28 | |
| Probable exosome complex exonuclease 1 | A. fulgidus | 3M7N:D | 0.9 | 59 | 2.33 | 33.33 |
| P. abyssi | 2PO1:A | 3.21 | 40.00 | |||
| 50S ribosomal protein L7Ae | A. fulgidus | 1RLG:A | 0.8 | 60 | 13.45 | 36.00 |
| M. jannaschii | 1SDS:A | 17.09 | 23.33 | |||
| 60S ribosomal protein L7 | S. cerevisiae | 3O5H:G | 1.9 | 47 | 1.23 | 1.65 |
| T. thermophila | 4A1C:V | 2.51 | 5.00 | |||
| STAR family quaking protein | C. elegans | 4JVY:A | 2.8 | 58 | 10.20 | 71.43 |
| H. sapiens | 4JVH:A | 8.61 | 63.64 | |||
| Retinoic acid inducible protein I | A. platyrhynchos | 4A2X:A | 1.7 | 55 | 3.05 | 14.29 |
| H. sapiens | 3NCU:A | 7.46 | 25.00 | |||
| Arginyl-tRNA synthetase | S. cerevisiae | 1F7U:A | 2.6 | 29 | 7.25 | 32.89 |
| P. horikoshii | 2ZUF:A | 6.20 | 32.05 | |||
| Pumilio mRNA binding factor | S. cerevisiae | 3 K49:A | 1.1 | 45 | 9.49 | 90.00 |
| H. sapiens | 2YJY:A | 7.43 | 90.00 | |||
| tRNA pseudouridine synthase B | E. coli | 1K8W:A | 1.8 | 34 | 11.31 | 54.55 |
| T. maritime | 1R3E:A | 10.36 | 70.59 | |||
| Signal recognition particle 19 kDa protein | M. jannaschii | 1LNG:A | 2.1 | 34 | 35.82 | 16.49 |
| S. solfataricus | 3KTW:A | 22.94 | 19.79 | |||
| Phenylalanyl-tRNA synthetase | T. thermophiles | 2IY5:A | 2.1 | 31 | 3.14 | 7.89 |
| H. sapiens | 3TUP:A | 4.58 | 25.00 | |||