Well the other way to think about the problem is that protein structure can be robust to sequence changes. Among natural proteins, proteins that look similar can differ up to about 70% in sequence identity (since evolution had a hand in making sure the structure stayed folded as the sequence diverged from its ancestor). So long as some critical members of the sequence are preserved, the protein folds roughly to the same structure. AlphaFold does take advantage of this since part of the algorithm looks for sequence alignments with known proteins.