A second binding cavity, which is a low-affinity site for histamine in one of the HBPs, is located at the end of the barrel that is closed off in other lipocalins.
They also employed the mouse P-gp crystal structure deposited in the Protein Data Bank [ 23] to model the receptor binding cavity, which was treated as both rigid and flexible.
It was suggested that the di-peptides were too small to discriminate between different binding cavities, which is consistent to the hypothesis of 'a small ball in a large hole'.
This part of CD36-FA binding site contains a cavity which is characterized by the presence of a hydrophobic segment [184 204 aa] and is probably associated with the cell membrane.
Leuther et al (1999) reported that structure of DNA-PKcs protein contains an open channel, similar to those seen in other double-stranded DNA-binding proteins, and a cavity which is large enough to accommodate ssDNA.
Moreover, we functionally analyzed amino acid residues involved in substrate binding and in the architecture of the intersubunit cavity, which is a known binding site for disulfide reductase inhibitors.
CALA has a long, tunnel like binding site, while the B. subtilis deacetylase has a small cavity which is part of a cleft on the protein surface.
The determination of the SMU.440 crystal structure revealed a cavity which is similar to that of hormone and especially polyketide binding proteins sharing the same fold, indicating a polyketide-like binding site in SMU.440 homologs.
The most striking feature of the three-dimensional structure of Bet v 1 is the presence of a large hydrophobic cavity, which is open to the exterior and probably functions as a ligand binding site [ 12].
27 Eventually, only 40% of the total binding cavity area was occupied by all docked compounds, reflecting the relatively large size of the active cavity, which is a well established characteristic of CYP3A4.
