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.
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].
Structural modeling has demonstrated that DMIs bind CYP51 at the sixth ligand of the heme group, and it has been suggested that the Y136F mutation confers resistance by obstructing the heme-binding site [ 21].
Overall, as depicted in this figure, the autoinhibition only barely obstructs the Rap binding site.
The autoinhibition occurs because the linker peptide that connects the Cdc25 catalytic domain with the EF domain obstructs the Ras binding site.
It has previously been shown that these antagonists are non-competitive inhibitors and do not directly obstruct the ATP binding site.
As can be seen, visualization of active site residues along with transformed ligand not only helps in understanding their role in catalysis, but also highlights how a negatively charged glutamate residue can potentially obstruct the ATP binding site.
Indeed, recent work suggests the primary role for Cyc8 Tup1 involves obstructing the activation domains of the DNA binding proteins responsible for its targeted recruitment [23].
