Sentence examples for binding pocket which is from inspiring English sources
One approach is to identify molecules that occupy the pterin binding pocket which is distinct from the pABA binding pocket that binds sulfonamides.
The first region is located at the entrance of the substrate binding pocket, which is characterized by a network of hydrogen bonds between the adenosine moiety of hexanoyl-CoA and the protein.
Like eukaryotic PTPases, YopH catalyzes the hydrolysis of the phosphate moiety of phosphotyrosine within a highly conserved binding pocket, which is also characterized by the closure of the so-called "WPD loop" upon ligand binding.
The conformation got from docking simulation implies that the substrate can form strong binding interactions with the catalytic zinc ion and the residues in the binding pocket, which is consistent with the previously catalytic assumptions (Luo et al. 2014; Gotthard et al. 2013).
It clearly indicates that these four residues locate in the Tir binding pocket which is formed by B, C, D β-sheets and the loop between D, E β-sheets (Figure 4B).
In these structures, the nicotinamide of the nicotinamide adenine dinucleotide phosphate cofactor is visualized outside of its binding pocket, which is exacerbated by RAB-propyl binding.
As expected, we observed both the hydrophobic pocket surrounding I230, which was the same as in the hSTINGG230I-DMXAA complex, and the hydrophobic interactions within the DMXAA binding pocket, which were the same as in the hSTINGS162A/Q266I-DMXAA complex.
In comparison with wild type, the calculated binding free energy and computational alanine scanning analysis demonstrated the importance of the residues of scFv anti-p17 in the binding pocket which are TRP50, ASN52, GLU57, MET100, LEU185, and LYS188 with the relative decomposed energy below −2.00 kcal/mol.
A raloxifene-guided optimization step of the model previously developed in our laboratory produced significant changes at the level of volume and area of the binding pocket, which were attributed to the different size and shape of raloxifene compared with the planar and symmetric TCDD scaffold.
RESULTS: In this study, molecular modelling and simulations coupled with site-directed mutagenesis indicated that the endogenously generated tumour suppressor C18-ceramide binds I2PP2A/SET through the hydrophobic-binding pocket, which is localized within the two anti-parallel beta sheet stabilized loops and an extended alpha helix, including the K209/Y122 residues.
These cryo-EM structures unequivocally pin-pointed the location of capsaicin-binding pocket, which is formed by S3, S4 and S4-S5 linker within the membrane (Fig. 1C and 1D).
