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Figure 3.
Figure 3. Structure and interactions of the nonapeptide
ligand in AppA. A, Electron density associated with the peptide
ligand in the binding pocket of AppA together with the modelled
nonapeptide. The map is calculated with coefficients
2F[obs]-F[calc] and a[calc], and the electron density displayed
is contoured at 0.8 standard deviation from the mean density of
the map. The ligand atoms are coloured according to atom type
with carbon in grey, oxygen in red and nitrogen in blue. The
amino (N) and carboxyl (C) termini are labelled. B, Stereo
cross-section of the AppA structure illustrating the nonapeptide
ligand and some of its surrounding residues in AppA. The ligand
is coloured green and protein atoms are coloured according to
atom type as described above and with sulphur in yellow. Water
molecules are represented by red spheres. C, The extended set of
interactions formed by Arg373 of AppA and the main chain of the
peptide. Residues 5-9 of the peptide are shown with
charge-charge/dipole interactions indicated by the dotted lines.
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