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Figure 1.
Figure 1. Quality of the Structure and Overall View of the
CDK2–CksHs1 Complex(A) Stereo view of the 2.6 Å
resolution omit Fo–Fc electron density map, contoured at 2σ,
showing the predominant cluster of hydrophobic residues forming
the binding interface. The coordinates of this region (5% of the
total number of atoms) were omitted and the protein coordinates
were refined by simulated annealing before the phase
calculation. Residues are labeled in white for CDK2 and in
yellow for CksHs1.(B) Ribbon diagram of CksHs1 (yellow) bound to
CDK2, with the N-lobe in purple and the C-lobe in blue and
green. The ATP molecule is displayed at the interface of the two
CDK2 lobes (white bonds with red oxygen and blue nitrogen atoms
as spheres) and is taken from the free CDK2 coordinates ([11]).
The functional structural elements are color coded for CDK2: the
β1–β2 loop, red; the disordered loop to the PSTAIRE sequence
in helix α1, asterisks; the T loop, white. Side chains forming
the phosphorylation sites in the β1–β2 loop (Thr-14 and
Tyr-15) and in the T loop (Thr-160) (orange bonds with red
oxygen atoms as balls), as well as the CksHs1 side chains
forming the conserved phosphate anion–binding site (β1
Lys-11, β2 Arg-20, β3 Trp-54, and β4 Arg-71) (white bonds
with blue nitrogen atoms as balls), are displayed. The CDK2
secondary elements involved in the binding interface are
highlighted (green), and CksHs1 loops β1–β2 and β3–β4
are labeled L1 and L3, respectively.(C) CksHs1 molecular
surface, colored with the residues buried to a 1.6 Å probe
radius in pale yellow, the nonburied residues in white, and the
phosphate anion–binding site in blue. A ribbon diagram of the
CDK2 molecule is shown with the color code and orientation as in
(B). A CksHs1 Cα trace (orange) is shown through the surface
and reveals that the buried residues cluster in the interior
concave face of the CksHs1 β sheet and in the β1–β2 and
β3–β4 loops, which envelop the CDK2 helix α5 and loop L14
(green).(D) CDK2 molecular surface, with buried residues in
helix α5 (green) and loop L14 (cyan); nonburied residues are
shown in white. CksHs1 residues involved in the binding
interface are shown (orange bonds with red oxygen, blue
nitrogen, and yellow sulfur atoms as balls) with a Cα trace
(yellow). CksHs1 residues in all four β strands participate in
the binding interface.
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