Overall docking and molecular interactions of RF and RF catabolites within MR1 A′-pocket. (A) Superposition of the TCR-MR1-RF catabolite crystal structures showing the RF and its catabolites within the MR1-binding cleft of the MR1-RF structure interacting with MR1-Lys43. (B–E) Electron density omit maps (green mesh) of (B) RF, (C) FMF, (D) lumiflavin, and (E) lumichrome contoured at 2σ. (F–J) Molecular contacts of (F) RF, (G) FMF, (H) lumiflavin, and (I) lumichrome with the residues of MR1-A′-pocket in the MR1-Ag structures. Shown in J is the superposition of RF (cyan) with 5-OP-RU (yellow; PDB: 6PUC), which both have ribityl tail that extends toward the α2 helix. (K–L) Superposition of lumichrome (green) with (K) Ac-6-FP (pink; PDB: 4PJ5) and (L) DB28 (salmon; PDB: 6PVC) within MR1 ligand-binding cleft. (M) Superposition of lumichrome within the MR1 ligand-binding pocket of MR1^R9H structure (PDB: 6W9V) showing the MR1 residues from MR1–lumichrome structure in green and MR1^R9H residues in yellow. MR1 and β2m are colored white and marine, respectively. Here, the cutoff for hydrogen bonds, salt bridges, and VDW interactions was set at 3.5 Å, 4 Å, and 4 Å, respectively. Ligands are colored as follows: RF, cyan; FMF, orange; lumiflavin, magenta; and lumichrome, green. The α and β chains of the AF-7 TCR are colored yellow and pale green, respectively.