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Figure 2.
Fig. 2. Structural analysis of the IQN17:2K-PIE1 inhibitor
complex. (A) IQN17, consisting of IQ (orange) and gp41 (N17,
gray) segments, with inhibitors (green, yellow, and purple)
located in the canonical gp41 binding pockets. The purple
inhibitor is mostly occluded in this view. (B) Omit map for
2K-PIE1 contoured at 3.0 x rmsd. Five of the eight pocket
residues (gray, HXB2 numbering) that make hydrophobic contacts
with 2K-PIE1 (green) are shown. Two hydrogen bonds (black) at
the binding interface are also shown. (C) Overlay of D10-p1
(slate) and 2K-PIE1 (green) superposed by alignment of the IQN17
trimers. Intramolecular disulfide bonds (solid yellow) are also
shown. (D) A slab view through the center of 2K-PIE1 (green)
reveals an intact hydrophobic core (black) that excludes water.
(E) A similar view of D10-p1 (slate) reveals the presence of
several water molecules (red) in its core that nearly form a
water channel. (F) End-on view of the complex (same color scheme
as A) in which the surface from the last three residues of IQN17
have been removed. This view illustrates the packing of the
inhibitor into the deep hydrophobic pocket. dK2 (blue),
equivalent to the N-terminal Lys in PIE7 used for cross-linking,
is highlighted.
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