Sentence examples for binding cavity by a from inspiring English sources
Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair of closely spaced disulfide bridges and a short helical segment within the loop.
We therefore used the E. coli GGT structure (2DBX) to generate a potential substrate binding cavity by creating a 6 Å radius around the bound glutamate (Fig. 3c).
To explain the inactivity of compounds 4s 4t, 5f 5g, 5i and 5s all the inactive compounds were also docked in the urease binding cavity by using MOE.
One of these positions (23), placed in the helix A of the OBP, might alter the size and shape of the binding cavity by modifying the position of the first disulfide bridge [ 19, 44]; for instance, D. melanogaster LUSH, which has the first α-helix in a more internal position than in A. mellifera ASP1, has also a small binding cavity.
It is interesting to note that the active ligands bind to an extended binding cavity in a very consistent pose compared to the lead compound (3) supported by both loss-of-function but also gain-of-function mutagenesis data as we have reported previously4.
A calreticulin molecular zipper, observed in all crystal lattices, could further extend this site by creating a binding cavity lined by hydrophobic residues.
GPCRs are characterized by having seven α-helices that span the plasma membrane and form a receptor with a binding cavity for a ligand; the extracellular segment may also be able to bind a ligand.
The binding cavity also contains a Cys138-Asp8-Lys96 motif evocating a cysteine-based catalytic mechanism.
A replacement of the large, hydrophobic tyrosine by the smaller, positively charged histidine is supposed to distort the hydrophobic packing of the binding cavity and by this to lead to a conformational rearrangement of the active site pocket.
Previous computational methods relied on building a binding cavity into a protein template found in nature.
