The spatial structure determination of large biomolecules is an essential first step in the understanding of microscopic biological processes and of relevance in further application, such as drug development. Exploiting the coupling to the internal nitrogen nuclear spin as a quantum memory in conjunction with the spin-dependent photoluminiscence of nitrogen vacancy centers in diamond, we propose a protocol that can be used to determine the structure of small pockets of nuclear C-13 spins in complex proteins down to the atomic scale. The spatial reconstruction procedure, the associated error and possible paths of further improvement are discussed.