The NMDA receptor is one class of ionotropic glutamate receptors, which are the primary mediators of excitatory neurotransmission in the central nervous system. As such, function and dysfunction of these receptors has been implicated in such physiological and pathological processes as learning and memory, strokes, Alzheimer disease, and Parkinson disease. Studies into the similarly structured AMPA-type glutamate receptor have revealed a relationship between the extent of closure of the agonist-binding domain cleft and activation of the channel, showing a structural mechanism for transduction of signal from binding of ligand to receptor activation. However, neither crystal structures nor more dynamics-based studies using ensemble FRET/LRET show such a correlation when examining the agonist-binding domain of the glycine-binding subunit of the NMDA receptor. Here, we use single molecule FRET to examine more closely the range of conformation states probed by the isolated agonist-binding domain. To perform this, we had to overcome the problem of immutable native cysteines, which resulted in non-specific labeling when using the conventional maleimide-conjugated fluorophores that are regularly used in protein-based FRET studies. Thus, we introduced the unnatural amino acid p-acetylphenylalanine, which contains a unique ketone functional group, at the sites which we wished to test, allowing for specific labeling of the protein. Doing this, we see that while the protein exhibits a peak probability around 33A when bound both to full agonist glycine and partial agonist ACPC, the protein bound to partial agonist probes a slightly broader range of states than full agonist. From these data, we can infer that while the agonist-binding domain may show similar average extents of cleft closure, irresolvable by crystallography or ensemble LRET, full agonists more narrowly restrict the range of conformational states probed to conformations that allow for channel activation.