For centuries, tuberculosis has been a worldwide burden for human health, and gaps in our understanding of its pathogenesis has hampered the development of new treatments. ESX-1 is a complex machinery responsible for the secretion of virulence factors that manipulate the host response. Despite the importance of these secreted proteins for pathogenicity, only a few of them have been structurally and functionally characterised. Here, we describe a structural study of EspK, a protein known to be essential for the secretion of other substrates and the cytolytic effects of ESX 1. SAXS data show that EspK is a large molecule with a maximal dimension of 228 Å. It consists of two independent folded regions at each end of the protein connected by a flexible unstructured region driving the protein to coexists as an ensemble of conformations. Limited proteolysis identified a small globular domain at the C-terminus of the protein consisting of a mixture of -helices and -strands, as shown by CD and SAXS. In contrast, the N-terminal portion is mainly helical with an elongated shape. Sequence conservation suggests that this architecture is preserved amongst the different mycobacteria species, proposing specific roles for the N- and C-terminal domain assisted by the central flexible linker.