A model of the HKalpha2a subunit of the rabbit colonic H+, K+ ATPase has been generated using the crystal structure of the Ca(+2) ATPase as a template. A pairwise sequence alignment of the deduced primary sequences of the two proteins demonstrated that they share 29% amino acid sequence identity and 47% similarity. Using O (version 7) the model of HKalpha2a was constructed by interactively mutating, deleting, and inserting the amino acids that differed between the pairwise sequence alignment of the Ca(+2) ATPase and HKalpha2a. Insertions and deletions in the HKalpha2a sequence occur in apparent extra-membraneous loop regions. The HKalpha2a model was energy minimized and globally refined to a level comparable to that of the Ca(+2) ATPase structure using CNS. The charge distribution over the surface of HKalpha2a was evaluated in GRASP and possible secondary structure elements of HKalpha2a were visualized in BOBSCRIPT. Conservation and placement of residues that may be involved in ouabain binding by the H+, K+ ATPase were considered and a putative location for the beta subunit was postulated within the structure.