Fig. 4. AF2 modeling of interactions involving significant changes in receptor conformation.

a Estrogen receptor alpha - peptide derived from nuclear receptor cofactor 2 (PDB ID 2b1z⁶⁶). Left: In the free receptor conformation (PDB ID 3ert⁶⁷) the C-terminal helix occupies the peptide binding site. Shown are the solved crystal structures of the unbound (blue) and bound conformation (receptor in white, peptide in green). Right: AF2 models the correct receptor conformation, and positions the peptide accurately in the binding site (RMSD < 1.0 Å). Shown are the AF2 model (unbound receptor: maroon, bound receptor: pale pink, peptide: magenta), compared to bound conformation (white). b EphB4 receptor––ephrin-B2 antagonist (PDB ID 2bba⁶⁸). Left: In the free receptor conformation (PDB ID 3etp⁶⁹) the J–K loop forms a β-hairpin. Right: Upon peptide binding, this hairpin becomes disordered and assumes a flexible loop conformation, which is recovered in the AF2 model. Coloring as in a.