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. 2023 May 3;14:2558. doi: 10.1038/s41467-023-38168-3

Fig. 5. Molecular model of DKP D/L isomerase NozR and NozR complex with substrate LL-cWW (3).

Fig. 5

a Superposition of the NozR model (gray) with homolog allantoin racemase (green, PDB 3QVJ) revealed secondary and tertiary structure conservation. b Superposition of the binding pocket surface for NozR (gray) with that of allantoin racemase (dark green) revealed an expanded pocket for NozR, predicted to accommodate the DKP group and bulky indole residues of cWW. c Docking of 3 (orange carbon atoms) with NozR indicated accommodation of both the DKP moiety and indole groups. NozR residues within 4 Å of 3 are rendered as licorice sticks and labeled. Sulfur atoms from Cys-75 and Cys-179 of the catalytic dyad are 3.7 Å and 4.2 Å, respectively, from C9 of 3. Supplementary Data 1 is a PDB file of this structure.