Table 2. Active site residues proposed for guided docking by HADDOCK. The structurally similar RNA-bound complexes used to identify interacting residues are given. If a related fold information was not used, ab-initio RNA prediction method used to predict binding sites, are listed. The residues proposed either based on structurally similar interactions or by ab-initio predictions, are listed in parentheses. Those added additionally to the list based on the vicinity to IRES RNA, are listed outside parentheses.
Ribosomal protein | Interface residues involved in docking restraints | Structurally similar interaction / Prediction | IRES bases |
---|---|---|---|
S5e | (V134,R136,R127), (T104,I178,K182,N186,Y188,K191,E195,R198,S202) |
2WDM-G, 2NOQ-F |
80–87, 67–73, 90–95, 97–101 |
S25 | K114,(K66,R76) | Muhs et al. 2011 | 80–87, 67–73, 90–95, 97–101 |
S26 | (R51,K66),Y62 | BindN | 305–308,329 |
S3a (S1e) | (K199, Q202) | RNABindR | 299,300 |
S27 | (K36,Y41,R80,Q83) | 3IZR-m | 234–237 |