N-methyl-D-aspartate (NMDA) receptors are ligand-gated channels important in neurotransmission which are activated by the combined presence of glutamate and glycine. They are comprised of four subunits that form a dimer of dimers. The activity of NMDA receptors is modulated by a variety of endogenous ligands such as zinc ions, phenylethanolamines, polyamines and protons. Findings show that the binding sites for these modulators are found in the amino terminal domain of such receptors, but different modulators appear to affect different subunits. However, despite the enormous efforts expended in mutagenesis and patch clamp experiments on NMDA receptors, the exact assembly of these subunits and the effects of the modulatory species are not well understood. We have modelled dimers of the amino terminal domains of these receptors based on their homology with the extracellular dimer of a metabotropic glutamate receptor. Conserved cysteine residues, which have been highlighted as important in previous work, are shown to form a disulphide bridge, stabilizing a four-helix bundle between subunits. This establishes a hinge in the receptor. The model also highlights a zinc binding site in the binding crevice of the NR2a subunit of the receptor that stabilizes the open state of the amino terminal domain. The similar effect of ifenprodil is thus explained by its stabilization of the open state of the amino terminal domain (ATD). The presence of three histidine residues in the zinc site is used to explain the pH dependence of zinc inhibition. Previous work has also implicated certain residues in spermine stimulation of such receptors. The homology model shows that this site is found at the inter-subunit boundary of the dimer. This predicts a binding site between subunits, a result not calculable by the homology modelling of single subunits done previously. Finally, these results are drawn together to yield a consistent picture of NMDA receptor activation and desensitization. An understanding of how these receptors work and how they can be modulated is an important step toward rational drug design.