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It is based on 3D coordinates only and does not use information about the binding site for ligand preparation or information about active ligands for the setup of the protein binding site.
The region showing higher 'j' density was identified to be the binding site for ligand.
These insertions may either act as embellishments or promote functional diversity by presenting altered/new binding site for ligand or macromolecule [38], [40].
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The binding site for ligands is buried in an interior cavity and surrounded by β-strands.
These insertions may promote functional diversity by creating a new binding site or by changing a present binding site for ligands or macromolecules (6, 7).
If the central cavities observed in TySemiSWEET and LbSemiSWEET represent the primary binding site for ligands in SemiSWEETs, two questions immediately stand out.
Consider a protein P with four binding sites for ligand X.
Several binding sites for ligand binding to CCK2 receptor have been identified in mutagenesis studies (Fig. 2) (Foucaud et al. 2008).
Hormone responsive elements (HRE) are super family of binding sites for ligand activated nuclear hormone receptors for thyroid hormone (TRE), retinoic acid (RARE) and vitamin D, which regulate gene transcription.
This work demonstrated that it had good selectivity over other proteins and it could be a useful strategy to detect other targets with two affinity binding sites for ligands as well.
The chapter also describes the discoveries related to signal transduction such as the discovery of hormones, chemical transmission of signals by neurotransmitters like acetylcholine, ergot alkaloids and other mind-bending substances, and receptors present in plasma membranes that are specific binding sites for ligands.
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