Much research has been published about trajectory management on the ground or at the sea, but compression or indexing of flight trajectories have usually been less explored. However, air traffic management is a challenge because airspace is becoming more and more congested, and large flight data collections must be preserved and exploited for varied purposes. This paper proposes 3DGraCT, a new method for representing these flight trajectories. It extends the GraCT compact data structure to cope with a third dimension (altitude), while retaining its space/time complexities. 3DGraCT improves space requirements of traditional spatio-temporal data structures by two orders of magnitude, being competitive for the considered types of queries, even leading the comparison for a particular one.