The three dimensional structure of a combining region-ligand complex of immunoglobulin NEW at 3.5-A resolution.

IgG New binds ligands such as orceine, menadione, and uridine with a low affinity (K(0) about 1 x 10(3) liter/mol) and a gamma-hydroxy derivative of vitamin K(1) with a higher affinity (K(0) = 1.7 x 10(5) liter/mol). Binding studies indicate that both the 2-methylnaphthoquinone rings and the phytyl tail of the vitamin K(1) hapten contribute to the total binding energy. The binding of these ligands in the crystalline state has been investigated by difference Fourier maps of Fab' New-ligand complexes at 6-A resolution. A 3.5-A resolution difference Fourier map obtained for the gamma-hydroxy derivative of the vitamin K(1)-Fab' complex shows that this hapten is bound in a shallow groove or crevice between the light and the heavy chains, in close proximity to the polypeptide segments containing the hypervariable regions. At least 12 amino-acid residues from both the light and the heavy chains appear to be in close contact with the ligand. No major conformational changes were detected in the Fab' fragment after ligand binding.