Catalytic site distances of predicted enzyme-enzyme complexes in E.coli

Supplementary material associated with publication: "Is metabolism spatially optimized? Structural modeling of consecutive enzyme pairs reveals no evidence for spatial optimization of catalytic site proximity." by Joaquin Algorta and Dirk Walther (currently under review, pre-print: doi.org/10.64898/2026.03.24.713955). Predicted complex structures of 107 sequential E.coli enzyme pairs, i.e. enzymes sequential reaction steps, and randomized enzyme pairings, using AlphaFold2, AlphaFold3, ESMfold, and HDOCK.

Pairs are indicated by their uniprot IDs, every pair contains the predicted structure (.pdb file) and a Pymol script (.pml) that starts a Pymol session with all relevant information (Euclidean distance and computed Shortest Accessible Space and associated distances. The developed computational procedures for computing Shortest Accessible Space Paths (SASP) between two sites on proteins have been made available at github.com/joacolongo/SASP.