Table 2

Comparison of binding grooves of CD1, MHC class I and II, and FcRn. The binding groove was defined as a set of atoms meeting each of three criteria (37): They must have ≥ 0.1 Å2 solvent accessibility to a 1.4 Å probe, ≤ 1 Å2 solvent accessibility to a 5 Å probe, and contribute atoms to the contiguous scribed molecular surface between or below the α1 and α2 helical axes and above the β-sheet platform. This definition differs subtly from previous definitions used to define the grooves of FcRn (22) and H-2Kb (5) in that the groove is considered as a set of atoms rather than a set of residues and only surface that contributes to the contiguous groove is part of the surface area. Row 2 shows the number of residues contributing to the groove molecular surface; row 3 gives the number of carbon atoms that these residues contribute to this surface; row 4 the number of polar atoms; and row 5 the number of charged atoms. Row 6 shows the surface area of the groove (37) and row 7 shows the MHC surface area buried (27) on ligand binding where applicable. The number of residues, hydrophobicity, and surface area are significantly larger in CD1, whereas the number of polar and charged atoms are fewer.

CD1d1*CD1d1H-2KbH-2DbHLA-A2HLA-B27H-2M3FcRnHLA-DR1
Residues464629302533392234
Carbon atoms10210850574662752953
Polar atoms910111691114913
Charged atoms1185610455
Surface area (Å2)13101390763763747891898509725
Buried surface (Å2) N.A.N.A.11821220116510621122N.A.1220
  • * Molecule 1 of the asymmetric unit.

  • Molecule 2 of the asymmetric unit.

  • The buried surface area (27) upon peptide binding. The buried surface area is greater than the groove surface area because it contains an appreciable area that would be excluded from the groove surface by the solvent accessibility criteria used to define the groove surface (37). The buried surface can be approximated by adding a 2.8 Å wide skirt to the groove surface. The surface area of this approximation of buried surface for H-2Kb is 1259 Å2, whereas the surface area for a similar surface for CD1d1 is 1756 Å2.