Extended Data Fig. 6: Contour map of Tyr46 side chain conformation of ABLE from molecular dynamics.
From: Emergence of specific binding and catalysis from a designed generalist binding protein
(a-b) Dynamics of uncomplexed ABLE (PDB: 6W6X) and ABLE-apixaban (PDB: 6W70) were explored by doing molecular simulation at 278 K for 500 ns with Amber. Chi1 and Chi2 from each state of these simulations and reported crystal structures of ABLEs (6W6X: uncompleted ABLE; 6W70: ABLE-Apixaban Complex; 6X8N: uncomplexed ABLE His49Ala) were extracted for plotting. Contours were generated from the frames of uncomplexed ABLE (a) and ABLE-apixaban complex contours (b) using an in-house script that utilizes the Gaussian kernel density estimate methods from scipy.stats module of SciPy Python Packages. (c-d) A and B conformations of Tyr46 sidechain were present in the uncomplexed ABLE crystal structure (c, PDB: 6W6X), while only A conformation of Tyr46 sidechain conformation was present at ABLE-apixaban complex (d, PDB: 6W70).
