tRNA docking

The EcTsaDB-tRNA complex model was generated by rigidly docking a tRNA molecule onto the EcTsaBD complex using the HADDOCK Server (version 2.2) (41). The tRNA structure was extracted from the crystal structure of threonyl-tRNA synthetase-tRNA complex (PDB : 1QF6) (42) in which the E. coli tRNA^Thr UGC contains a m⁶t⁶A at position 37 in the anticodon loop. For docking, the m⁶t⁶-moeity and other modifications were removed from the E. coli tRNA^Thr UGC. The docking protocols and parameters follow the default settings for protein-RNA complexes in HADDOCK. As for the direct contact sites, critically, His111 and His115 in EcTsaD were specified as active site residues in the receptor molecule whereas A37 was specified as substrate in tRNA. By default, the active sites-surrounding residues were specified as passive. Resulting models were ranked based on scoring performance and clustered. The first model from the top-ranked cluster was chosen to represent the structures.