Fig 3.
Structural analysis of the NNTD surface. (A) RMSFs of the protein backbone reveal three flexible regions of the core of the fragment encompassing residues 31 to 252 of HRSV N. The putative pockets PI and PIII are defined by members whose backbone is rigid (the RMSF is less than 0.5 Å), while PII and PIV share flexible turn 1 (FT1) and FT2 of the protein, respectively. For clarity, the residues defining PI and PIII are not represented on the RMSF curve but rather on two straight lines. (B) Four pockets were identified by the Surflex molecular docking package. The protomols defining the four pockets are represented through their solvent-accessible surfaces. PI (pink) is surrounded by flat areas, while PII (cyan) and PIV (blue) are located at sharp edges of the protein, having FT1 and FT2 (orange) as components. PIII (red) is an extension of PI.