Biomolecules & Therapeutics : eISSN 2005-4483 / pISSN 1976-9148

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Fig. 1. The ligand binding site of SARS-CoV-2 N protein for the computational docking simulation. (A) The assembly model of the SARS-CoV-2 N protein dimer structure is shown within the viral ribonucleoprotein based on the public cryoelectron tomography model of SARS-CoV-2 (EMD-30429, EMD-30430). (B) The three domains of the N protein dimer constructed by AlphaFold are shown: N-terminal domain (NTD) in red, C-terminal domain (CTD) in green, and an intrinsically disordered central Ser/Arg (SR)-rich linker (LKR) in grey. The ligand binding site of the NTD was defined as a 30 Å sized grid box (shown as gray box) centered on the average centroid of the known RNA binding site of NTD monomer structures. TYR109 residue was located near the center of the grid box and marked as magenta. The interaction model of AMP (blue) and the TYR109 residue of the N protein NTD. The base of AMP was shown to interact via π−π stacking interaction with the TYR109 residue in the docking simulation. All 3D molecular graphics were conducted using the PyMOL software and UCSC Chimera X.
Biomolecules & Therapeutics 2022;30:427~434
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