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How does someone determine if the ligand binding pocket is shallow or deep? Specifically between 4XAD...

How does someone determine if the ligand binding pocket is shallow or deep? Specifically between 4XAD and the ligand.

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Answer #1

Ligand binding ability tells about the efficiency of producing biological response upon binding with the target receptor.

Here 4XAD is an Egg white Lysozyme. 4XAD acts a catalyst in the hydrolysis of two sugars which make up the bacteria wall. These two sugars are β-(1,4) glycosidic bond between N- acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).

The ligand which is used to bind this enzyme is a saccharide compund consist of two rings combined by oxygen atom. The ligand name is 2-(acetylamino)-2-deoxy-4-O-beta- D-galactofuranosyl-alpha-D-glucopyranose. Therefore it is logical to say that lysozyme would bind it given the enzyme’s relationship to the glycosidic bond between NAG and NAM.

The ligand binding pocket will be SHALLOW as the ligand is exposed open to the solution and not completely enclosed by the protein.

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