Fig. 5: Performance of Re-Glyco on AlphaFold structures.

a, A histogram analysis of the distribution of pLLDT scores of residues clashing during the GlcNAc Scanning of 3,415 proteins from the AlphaFold Protein Structure Database, with a total of 12,789 glycosylation sites annotated in Uniprot. The distribution of pLDDT values for all residues in the protein tested is shown with a dashed line. The distribution of the pLDDT values for the residues clashing with the GlcNAc during GlcNAc Scanning, where clashes were resolved by Re-Glyco is shown with powder blue histograms and a blue line. The distribution of the pLDDT values for the residues where clashing was not resolved by Re-Glyco and for the residues in the immediate vicinity (±2) is shown with rose histograms and a red line. b, The 3D structure of the EXTL3 monomer from PDB 8OG1 (green cartoons) represented within the homodimer from PDB 7AU2 (white surface). The resolution for each structure is shown in the labels. Asn residues within sequons are shown with van der Waals (vdW) spheres, where N atoms are in blue and O atoms are in red. The N-glycosylation sequons known to be occupied are shown in bold. A green check mark indicates that the site is predicted to be occupied by Re-Glyco, while a red cross mark indicates that the site is predicted to be unoccupied by Re-Glyco owing to major steric clashing. c, Bottom: the 3D structure of the EXTL3 monomer from AlphaFold (AF-O43909-F1) shown in cyan. The lowest-confidence loops and termini are removed from the image for clarity. The all-atom RMSD versus PDB 8OG1 is shown in the label. Top: a close-up view of the sidechain orientation of Asn 592, where the clash with a spatially neighboring loop prevents functionalization. d, Bottom: the 3D structure of the EXTL3 monomer from ColabFold (Rank 001) shown in orange. Top: a close-up view of the sidechain orientation of Asn 592, showing the alternative orientation that allows for functionalization. Molecular representation with pymol (https://pymol.org/2), and statistical analysis and rendering created with matplotlib (https://matplotlib.org/).