Synapse-associated protein 97 (SAP97) is a membrane-associated guanylate kinase protein that interacts with other proteins such as ion channels, subunits of glutamate receptors, and other cytoskeletal proteins and molecular scaffolds. The molecular diversity of SAP97 results from alternative splicing at the N-terminus, and in the U1 and U5 regions. There are two main N-terminal isoforms: the β-isoform has an L27 domain, whereas in the α-isoform, this is replaced by a palmitoylation motif. We have used multiangle light scattering, nuclear magnetic resonance, and small-angle X-ray scattering studies to characterize the conformation of a truncated form of the β-isoform, hence mimicking the α-isoform. This paper provides a comprehensive view of the small-angle X-ray scattering data, and the resulting data show that the scattering data are consistent with the presence of an ensemble of forms in dynamic equilibrium, with two prominent populations of compact and extended forms, with R(g) values of 38 ± 7 Å (52%) and 70 ± 10 Å (37%), respectively. The data show that without the L27 domain, the conformation of SAP97 is biased toward the compact form. We propose a hypothesis in which the overall conformation of SAP97 is determined by the nature of the N-terminus, which may, in turn, influence the specific role of a particular splice variant.