However, Brown and collaborators have subsequently shown that these sites are involved in peptide-binding pockets that are crucial for peptide capture (Stern et al. 1994).
Upon inspection of the Parkin structure, we identified two further putative phospho-Ser-binding pockets that we term "Pocket 2" and "Pocket 3" (Fig 2A).
Detailed analysis of the dissociation processes of inhibitors from the PR binding pocket showed that the different binding strength was caused by the difference in the stability of H-bond networks in the bound complexes.
Examination of the ADP/ATP binding pocket shows that it adopts a conical topology in which the entrance is wide open and the bottom of the cavity very narrow and very likely to tolerate small groups only.
Docking of the pheromone and analogs onto models of the two known PBPs of the gypsy moth revealed that the internal binding pocket of PBP1 showed higher selectivity than that of PBP2, consistent with in vitro binding assays.
As it concerns the GPER ligand binding pocket, visual inspection showed that it lies within a deep cleft in where 10 hydrophobic residues (V116, Met133, Leu137, Phe206, Phe208, Phe 278, Ile279, Ile308, Val309 and Phe314) and 5 polar amino acids (Tyr123, Gln138, Asp210, Glu275 and His282) contribute to stabilize the ligands through Van der Waals interactions and hydrogen bonds, respectively.
A docking simulation involving the proposed minimum sequence in the receptor binding pocket of HA showed, that the side chains of the amino acids of the peptide utilized the same hydrogen bonds and van-der-Waals interactions to HA as the natural binder sialic acid [ 4].
Interestingly, the 2.8-Å structure shows electron density in this putative nucleotide-binding pocket that we interpret as a bound sulphate ion.
