Fig. 3: Categorization of residues into groups G1-G5 based on PC scores.

a Legend defining groups G1-G5, each corresponding to a distinct dynamic mechanism, captured by the first three principal components derived from spectral density data. b Chart showing changes in numbers of residues assigned to each group when comparing the apo and ligand bound states. c–e Structural mapping of classified residues onto MurD crystal structures: G1 (orange), G2 (blue), G3 (yellow), G4 (pink), and G5 (green). Left panels show PC score plots derived from the standardized data on J(0), J(ω_N) and J(0.87ω_H) for MurD_apo. Circles denote the data points for the PC scores, with colored circles indicating residues assigned to G1-G5 based on classification criteria (Table 2), while unfilled circles indicate residues not assigned to any group. Colored cones define the classification regions in PC space which comprise the residues of a particular group. Right panels display the crystal structures of MurD in three conformational states: the open conformation of MurD_apo (left, PDB 1E0D²¹), the semi-closed conformation with ATP (magenta) for MurD_ACP (middle, PDB 8VW2²²), and the closed conformation with inhibitor 1 (forest green) for MurD_inh (right, PDB 2XPC¹¹). Note that G4 and G5 group of residues for MurD_inh contains somewhat different information than for the other two states, as indicated above. Residues shown in grey have no group assigned, while residues shown in white indicate unavailable data.