LlPR‐10.2B, a Pathogenesis‐related class 10 (PR‐10) protein from yellow lupine (Lupinus luteus) was crystallized in complex with melatonin, an emerging important plant regulator and antioxidant. The structure reveals two molecules of melatonin bound in the internal cavity of the protein, plus a very well‐defined electron density near the cavity entrance, corresponding to an unknown ligand molecule comprised of two flat rings, which is most likely a product of melatonin transformation. In a separate LlPR‐10.2B co‐crystallization experiment with an equimolar mixture of melatonin and trans‐zeatin, which is a cytokinin phytohormone well recognized as a PR‐10‐binding partner, a quaternary 1 : 1 : 1 : 1 complex was formed, in which one of the melatonin‐binding sites has been substituted with trans‐zeatin, whereas the binding of melatonin at the second binding site and binding of the unknown ligand are undisturbed. This unusual complex, when compared with the previously described PR‐10/trans‐zeatin complexes and with the emerging structural information about melatonin binding by PR‐10 proteins, provides intriguing insights into the role of PR‐10 proteins in phytohormone regulation in plants, especially with the involvement of melatonin, and implicates the PR‐10 proteins as low‐affinity melatonin binders under the conditions of elevated melatonin concentration.DatabasesAtomic coordinates and processed structure factors corresponding to the final models of the LlPR‐10.2B/melatonin and LlPR‐10.2B/melatonin + trans‐zeatin complexes have been deposited with the Protein Data Bank (PDB) under the accession codes 5MXB and 5MXW. The corresponding raw X‐ray diffraction images have been deposited in the RepOD Repository at the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM) of the University of Warsaw, Poland, and are available for download with the following Digital Object Identifiers (DOI): https://doi.org/10.18150/repod.9923638 and https://doi.org/10.18150/repod.6621013.