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In both structures, the ATP mimic nestles deeply into the ATP cleft; in contrast, the peptide substrate mimic sits in a much shallower, solvent exposed cleft.
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Surface exposed clefts as well as buried cavities are defined by the union of overlapping spheres and are roughly sorted by volume.
French artist Gustave Courbet's 1866 painting, L'Origine du monde (The Origin of the World), provoked a huge scandal not only because it exposed the "cleft of Venus" but also because it portrayed a woman's vagina in its full hairy glory, rather than classically bare.
The results described above suggest the cleft exposed in the rhodopsin cytoplasmic face exposed by TM6 movement provides part of the interface for interaction with arrestin.
All identified mutations map to residues forming intra-repeat loop 2, which is also termed the substrate specificity loop and is located within the exposed substrate-binding cleft (Fig. 1B).
The most likely mode of binding involves the finger loop docking into the cleft exposed in the rhodopsin cytoplasmic face upon receptor activation and TM6 movement, as shown in Figure 6A.
Upon binding of prorenin to (P RR, the prosegment covering the active site of prorenin becomes unfolded, and the enzymatic cleft exposed, activating prorenin in a non-proteolytic way [ 14] (Fig. 1).
NAD(P H is bound in a solvent-exposed cleft, allowing facile replacement.
However, the shorter asparagine side chain creates a small cleft exposing the charge of the E163 carboxyl group.
Plausibly MyD88 might displace the 'E' helix from Mal and bind into the cleft that is exposed (Figure 5A D).
Glu294- Arg367 (Pair 1) was solvent exposed in the active site cleft and both residues were important for stabilization of phosphate on ATP and the activation loop [21], [24], [25], [33], [34].
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