Skip to main content
. 2020 Sep 17;12(9):602. doi: 10.3390/toxins12090602

Figure 1.

Figure 1

(A) Three-dimensional (3D) structure comparison by MATRAS of M protein epitope with S1 protein. M epitope sequence (SecB) is not similar to S1 RBD with only one residue in common (marked with an “*”), yet the structure is similar (depicted in rainbow colors). (B) Top model generated by CoDockPP of RTAM-PAP1 (magenta, RTAM being on the upper left side) in complex with M protein (in rainbow colors). (C) Top model generated by HADDOCK2.2 with a score of −163.8 (±8.3). PAP1 is on the left side to denote its more important role than in other models and RTAM on the right side (from right to left, N to C terminal in blue to red). M protein is on top and in less solid rainbow colors (N to C terminal in blue to red). (D) The top model generated by ZDOCK with RTAM-PAP1 in backbone format (N to C terminal in blue to red). The colored disks depict the binding contact sites. The disks indicate where the van der Waals radii of atoms overlap and the colors how close the contact is: yellow = close, orange = touching, and red = overlapping (models viewed using Jmol).