Highly diverse regions including the two residues following the KNRY motif and the topology of the secondary substrate-binding pocket present in a number of PTPs contribute to defining substrate specificity.
To further validate the notion that under semi-native PAGE conditions TTR runs as a tetramer, we used the small molecule resveratrol that, by virtue of binding in the T4 binding pocket present only in the native tetramer, becomes fluorescent.
While the pTyr-binding pocket, which is present in the N-terminal half and highly conserved in the SH2 domain, provides the basal affinity for ligand binding with approximately a half of the total binding free energy [ 62], the hydrophobic pocket present in the C-terminal half of an SH2 domain provides specificity towards a hydrophobic residue in a peptide ligand.
It has several binding sites on each fibrinogen-like domain: an outer binding pocket, also present in H-and M-ficolins, together with three unique sites, which form a continuous binding surface for various acetylated and neutral carbohydrate ligands.
By "biological affinity," binding of ligands or proteins to specific binding sites or pockets present in target proteins (e.g., receptors or enzymes) is meant.
Only a single methyl-lysine-binding pocket is present in all MBT-repeat proteins, whereas the corresponding 'pockets' in the other repeats are shallower and less well conserved.
Sequence alignments using the identified β-valinyl CoA ligase, PaaK1 and PaaK2 demonstrated that the ATP-binding pocket is present in the identified β-valinyl CoA ligase.
Residues 115 and 142, involved in the rearrangement of the loop 112 120 at the entrance of the substrate-binding pocket and present in all ADH7 forms, are also included.
The structure of NPC1L1 NTD) reveals a slightly larger binding pocket than is present in NPC1 NTD) allowing for broader sterol specificity than NPC1 [15], [15], in particular sterols with substitutions at C4 (Fig. 4C).
