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. 2020 Sep 23;11:4808. doi: 10.1038/s41467-020-18619-x

Fig. 4. Computational design of HG4 on various backbone templates.

Fig. 4

The HG4 crystal structure with bound 6-nitrobenzotriazole (white) is overlaid on the HG4 design models (colored) obtained using the crystal structure of (a) HG4 with bound 6-nitrobenzotriazole, b Thermoascus aurantiacus xylanase 10 A (PDB ID: 1GOR), c HG3 with bound 6-nitrobenzotriazole, or (d) HG3 without 6-nitrobenzotriazole. e–h the HG4 design models obtained using the template prepared by ensemble refinement or unconstrained molecular dynamics (MD) that gave the best energy following repacking. PHOENIX energies of design models after repacking are indicated at the bottom right. For reference, the energy of the HG4 crystal structure with a bound transition state is −186.7 kcal/mol. In all cases, the transition state and transition-state analogue are shown at the center of the barrel. Side chains of all residues forming the binding pocket are shown with the exception of Ala21 and Pro45, which were omitted for clarity. The sphere shows the alpha carbon of Gly83. Asterisks indicate residues that adopt side-chain rotamers varying by >20 degrees around one or more side-chain dihedrals between the design model and crystal structure.