Fig. 4: ECHT decomposition of a structure of the SARS-CoV-2 main protease (7k3t).

The protein is shown as lines and ellipsoids, coloured by B-factor for each structure independently from blue (zero) to green to red (maximum); the symmetry-related copy creating the obligate homodimer is shown as semi-transparent surface. The binding site histidine (HIS 41) is also shown as a semi-transparent surface, and as sticks in both monomers. B-factor ellipsoids are contoured at p = 0.95. a Re-refined structure from PDB_REDO²¹ (1.2 Å resolution; R_work/R_free 0.14/0.16; refined with a-ADPs; B-factors 7.7–77.6 Ų). b–f Disorder components of each ECHT level (maximum B-factor in brackets): b chain (7.4 Ų), c secondary-structure (30.2 Ų), d residue (35.9 Ų), e backbone & sidechain (14.4 Ų) & (f) atomic (19.0 Ų). c, d Flexible segments and residues line the sides of the catalytic site (see also Supplementary Fig. 1). c The P2 helix, on the edge of the catalytic site, shows a large disorder component at the secondary-structure level. The C-terminal also shows a large disorder component (see Supplementary Fig. 2). d The P5 loop is also observed to be particularly flexible in the residue level. e Backbone motions are generally small, with the majority of disorder being isolated to the surface side chains. f Atomic disorder highlights internal motions of residues that cannot be modelled by the rigid-body approximation; these principally highlight longer side chains and backbone carbonyls, as well as presumably absorbing inflated B-factors from modelling errors. Images rendered in pymol²⁹.