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Figure 2.
Figure 2. Structure of Nef–SH3 Complex(A and B) Stereo
diagrams of the polypeptide backbones of Nef[core] and Fyn(R96I)
SH3. The N-terminal helical layer of Nef[core] (residues
71–120), which forms the SH3 interaction surface, is colored
yellow. The rest of Nef[core] (residues 121–203) is colored
green. The disordered loop (residues 149–178) between βC and
βD is indicated as a dotted line. The Fyn(R96I) SH3 domain is
in blue. Also shown are the side chains of the conserved
tryptophan of SH3 (residue 119, in red), the
specificity-conferring isoleucine of SH3 (residue 96, in red),
and the two prolines that define the PxxP motif of Nef (residues
72 and 75, in yellow). The views in (A) and (B) are
approximately orthogonal. The figure was prepared using
MOLSCRIPT ([23]) and Raster3D ( [1]).(C) The molecular surface
of Nef[core], with Fyn(R96I) SH3. The local electrostatic
potential of Nef[core] was calculated in the absence of the SH3
domain using GRASP ([27]). The molecular surface is colored
according to the local electrostatic potential, with colors
ranging from dark blue (most positive region) to deep red (most
negative) through white (neutral). The SH3 domain is shown as a
blue tube. The side chains of Trp-119 and Ile-96 of SH3 are
shown in yellow. Trp-113 and Phe-90 of Nef separate the binding
pocket for Ile-96 of SH3 from the hydrophobic crevice that is
available for potential interaction with other molecules.
Arg-106 of Nef, located at the lower left edge of the crevice,
is implicated in the association of Nef with a Ser kinase
activity ( [33]).
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