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. 2019 May 21;116(23):11470–11479. doi: 10.1073/pnas.1903675116

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Fig. 3. — The structure of GerK₃A^NTD is similar to those of PeBP proteins. (A) Superimposition of the N1 domain of GerK₃A^NTD (red) and the domain 2 of OpuAC (green; PDB ID code 2B4L). The bound ligand for OpuAC, glycine betaine, is shown in space-filling representation. (B) Molecular surface representation of the two interfacial pockets (cyan) between the N1 (red) and N2 (gray) domains of GerK₃A^NTD defined by HOLLOW (66). (C) One of the top-ranked poses of the glucose molecule determined by AutoDock Vina is shown as licorice sticks in the presumed binding site in GerK₃A^NTD. (D) Molecular surface representation of the interface between the N1 and N2 domains of GerK₃A^NTD colored according to the local electrostatic potential (−5 kT to +5 kT), calculated with the program ABPS (65).