Structural Insights into Ligand Recognition by the Pleiotropic Odorant-Binding Protein AgamOBP9 - MD datasets

The dataset contains the raw data used to prepare the figures and plots of the article, which are related to the molecular dynamics (MD) study of AgamOBP9 in complex with ligands.
• The two PDB files OBP9-PMD_rep-MD1 and OBP9-PMD_rep-MD2 are representative snapshots (the cluster centroids) of the two most populated clusters obtained from hierarchical agglomerative clustering of ~28,000 snapshots from the 4 MD simulations of OBP9 in complex with PMD (p-menthane-3,8-diol). The two snapshots superimposed with the X-ray structure of OBP9 complex with PMD were used to generate Figure S9.
• RMSD_OBP9_CA.csv contains the root-mean-square deviation (RMSD) from the initial state of ligand-free OBP9 Cα atoms as a function of frame obtained every 10 ps of the 4 individual MD simulations performed.
• RMSD_OBP9-[BC|BC-MPD|ME|PMD]_CA.csv are the RMSD values of OBP9 Cα atoms from the corresponding MD simulations with bound n-butyl cinnamate (BC), n-butyl cinnamate in the presence of 2-methyl-2,4-pentanediol (BC-MPD), methyl eugenol (ME) and PMD (p-menthane-3,8-diol). These data were used to prepare Figure S7.
• RMSD_OBP9-[BC|BC-MPD|ME|PMD]_LIG.csv are the RMSD values of the ligand heavy atoms from the corresponding MD simulations, 4 for each system. These data were used to prepare Figure S6.
• RMSF_OBP9.csv contains the root-mean-square fluctuations (RMSF, or Cα atomic fluctuations) per residue of OBP9 obtained from 4 MD simulations of ligand-free OBP9.
• RMSF_OBP9-[BC|BC-MPD|ME|PMD].csv contain the per-residue RMSF values of each ligand-bound OBP9 system, for which 4 MD simulations were performed. These data were used to prepare Figure S8.