Traditional agricultural practices, such as classical plant breeding and pest management, have been utilized for many years to increase crop yield and improve its properties. However, more effective and sustainable practices are needed to meet the increasing global demands for agricultural-based products. In the past decades, DNA recombinant technology, and protein structure determination have been employed as a tool for the development of the agricultural field. Protein structure determination enables us to understand the structure-function relationship of a given protein, such as plant hormone, receptor, or growth regulators, thus introducing modifications to improve the properties of the crop. This review introduces the latest development of protein structure determination techniques ranging from X-ray crystallography, protein NMR, and cryo-electron microscopy. Notable examples of how these techniques can be utilized as a powerful tool for the sustainable development of the agricultural field, including their potential relevance in Indonesia, are introduced.