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Figure 3.
Figure 3. The proposed peptide binding channel. a, The
solvent accessible surface of SecB. On the left, the exposed
surface is colored based on the underlying atoms: all backbone
atoms, white; all noncharged polar and charged chain atoms (Asn,
Gln, Ser, Thr, Cys, Asp, Glu, Arg, Lys and His), blue; all
hydrophobic side chain atoms (Ala, Val, Leu, Ile, Pro, Phe, Tyr,
Trp and Met), yellow. On the right, the exposed surface
encompassing the two proposed peptide binding subsites is
highlighted. b, Ribbon drawing of the SecB tetramer viewed from
the side of the molecule. The orientation is the same as in (a).
The two subsites are shown in two zoom-in views. Residues lining
subsite 1 are colored purple and those lining subsite 2 are
colored cyan. For the purpose of clarity, only one subunit was
drawn in each of the zoom-in views. The residues lining the two
sites are all hydrophobic with the exception of Thr 53. c,
Schematic drawing of a PTB domain and a SecB monomer. The shared
structural motif is highlighted in gray. The peptide binding
sites are represented by hatched rectangles. Grasp36 was used to
produce (a); Molscript34 and POV-ray35 were used to produce (b).
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