Extended Data Fig. 7: Investigating the source of the AF-Cluster prediction for an alternate state of Mpt53.

a) plDDT vs. RMSD for AF-Cluster sampling on oxidoreductase Mpt53. Each prediction coloured by MSA size. b) plDDT values for state 1, corresponding to the known thioredoxin-like state, and an alternate unknown state are significantly higher than background. Box plots depict median and 25/75% interquartile range, whiskers = 1.5 *interquartile range. P-values for sample comparisons with p < 0.05 indicated, calculated via a two-sided test for the null hypothesis that 2 independent samples have identical mean values. n = 1642 models total. c) The conserved CxxC active site is very similar between its conformation in the crystal structure and models for the putative alternate state. d) Workflow for using DALI⁹¹ to screen for structure homologues to both Mpt53’s original state and predicted alternate state to search for any similar structures in the PDB that might have been in AF2’s training set. e) Plotting RMSD normalized by alignment length to both structures reveals some structures with lower weighted RMSD to the alternate state than to the original state. f) 7 of 9 DALI hits with lower alternate state RMSD contained an alpha-helix positioned in similar same way as in the Mpt53 alternate state (coloured in green). One structure (3EMX) also contained an N-terminus beta-strand positioned similarly to the alternate state.