Figure 5. Tertiary Interactions between Nef[core] and
Fyn(R96I) SH3 Domain(A) Molecular surface of Nef, showing the
binding site for the isoleucine side chain of the SH3 domain.(B)
Comparison of the interactions in the two complexes in the
crystal. The polypeptide backbones of Nef and the SH3 domain
are shown as green and blue tubes, respectively. Side chains of
Nef are shown in pink and in yellow (displayed under their
respective molecular surfaces). SH3 side chains are shown in
red. Hydrogen bonding interactions are shown as dashed lines.
Hydrogen bonds to backbone positions are indicated by the
placement of white circles along the backbone ribbon. For
clarity, the side chain of Ile-96 is not shown, and instead the
Cα position of this residue is indicated with a red circle. The
structure on the left is the complex that is the focus of the
major part of the discussion in the text. The structure on the
right is that of the second independent complex in the crystal.
Note the slight change in the relative orientation of the Nef
and SH3 components of the complex (see text). The side chain of
Asp-86 forms a hydrogen bond with Thr-97 in the RT loop of the
second complex. For clarity, this interaction is not shown.
The above figure is reprinted
by permission from Cell Press: