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The crystal structure of the human selenocysteine-containing protein glutathione peroxidase 4 (GPX4) was determined at 1.0 Å resolution. A mass-spectrometry-based approach was developed to monitor the formation of adducts of the active-site selenocysteine Sec46 with covalent inhibitors. The crystal structure of Sec46-containing GPX4 in complex with the covalent inhibitor ML162 [(S)-enantiomer] was determined at 1.54 Å resolution., Wild-type human glutathione peroxidase 4 (GPX4) was co-expressed with SBP2 (selenocysteine insertion sequence-binding protein 2) in human HEK cells to achieve efficient production of this selenocysteine-containing enzyme on a preparative scale for structural biology. The protein was purified and crystallized, and the crystal structure of the wild-type form of GPX4 was determined at 1.0 Å resolution. The overall fold and the active site are conserved compared with previously determined crystal structures of mutated forms of GPX4. A mass-spectrometry-based approach was developed to monitor the reaction of the active-site selenocysteine Sec46 with covalent inhibitors. This, together with the introduction of a surface mutant (Cys66Ser), enabled the crystal structure determination of GPX4 in complex with the covalent inhibitor ML162 [(S)-enantiomer]. The mass-spectrometry-based approach described here opens the path to further co-complex crystal structures of this potential cancer drug target in complex with covalent inhibitors.