PDBinder performance on the apo form of rRNA methyltransferase (KsgA). The binding site of the 16S rRNA methyltransferase (KsgA) from Thermus thermophilus in complex with 5'-methylthioadenosine (MTA). The holo form (PDB:3fut) is represented in yellow while the apo form (PDB:3fux) is in green. In order to evaluate the structural differences between the holo and apo forms, we superimposed the binding pocket residues (Residues 25, 27, 28, 54, 56, 75, 76, 99, 100, 117, 119) on their C-alpha atoms resulting in an RMSD of 2.05 Angstrom. Superimposed residues with an RMSD lower than 0.7 Angstrom are not represented in the picture (residues 54, 56, 75). PDBinder was able to identify all the binding residues of the holo form with the exception of Ala100 and Pro119. However, due to the high degree of conformational change, PDBinder did not identify residue Phe25 as binding in the apo form (RMSD 5.9). Even if the overall structure of the binding pocket is altered when the ligand is bound, the local conformation of small subsets of residues is mostly preserved and the method is able to identify seven of the eleven binding residues.
Bianchi et al. BMC Bioinformatics 2012 13(Suppl 4):S17 doi:10.1186/1471-2105-13-S4-S17