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A prominent feature of cyclin K is an additional helix (H4a) in the first cyclin box that obstructs the binding pocket for the cell-cycle inhibitor p27Kip1.
The latter orientation obstructs the binding site for Cc, because of the barrier imposed by the lipid bilayer.
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Attempts to co-crystallize aL2 with its antigen or to diffuse ampicillin into the wild-type aL2 crystals were unsuccessful, since crystal contacts obstruct the binding pocket.
Ct extension in SiCYS/Group II phytocystatins presumably did not obstruct the binding of its Nt region to papain, but improves the inhibitory activity against papain bases on the studies with CeCPI (Wang et al. 2008) and SiCYS here.
Conversely, the sensitizer (e.g., Bad) could obstruct the binding of Bax to Bcl-2.
A negative cooperativity can be understood in terms of the initial binding of one ATP obstructing the binding of the second ATP in the aptamer.
Among the ~28 million CpG dinucleotide sites that are susceptible to methylation in the human genome, approximately 10% are in the promoter regions of genes, in which they may physically obstruct the binding of transcriptional proteins to the gene or may be indirectly regulated by the recruitment of methyl-CpG-binding domain proteins through cytosine methylation [ 14- 16].
Overall, as depicted in this figure, the autoinhibition only barely obstructs the Rap binding site.
The inhibitory glutamate in aforementioned helix obstructs the ATP binding site and hence inhibits AMPylation by the Fic domain.
The autoinhibition occurs because the linker peptide that connects the Cdc25 catalytic domain with the EF domain obstructs the Ras binding site.
Probably, this mutations results in disruption of the packing, weakening distinctive structural features observed in the ALK structure, such as the unique inhibitory position of the ALK A-loop packing a short proximal A-loop α-helix against the αC-helix of ALK, while a β-turn motif obstructs the substrate binding region (Fig. 1B).
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