Insights into remdesivir intervention on SARS-CoV-2 polymerase and its broad-spectrum implication. Wu et al.
A modeled conformational transition in translocation. The video starts with an EV71 RdRP EC pre-translocation structure (PDB code 5F8M), through the first intermediate structure (PDB code 5F8N) and then the second intermediate structure (6LSH), and finishes with a post-translocation structure (5F8L). The coloring scheme and structure representations are the same as in Fig. S7. In order to generate this movie, the nucleotides of the last two states were mutated to match those in the first two states. The movie was generated using PyMOL (The PyMOL Molecular Graphics System, Schrödinger, LLC).
Steps to reproduce
1. Obtain PDBs (5F8M, 6LSH, 5F8L) from the Protein Data Bank. 2. Perform maximum-likelihood superpositioning by THESEUS. 3. Generate the video using PyMOL.