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The substrate binding cavity is a "pocket" located in the backrest.
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The binding cavity is formed within a four-helix bundle structure at the intersubunit interface, with two helices provided by each monomer.
The binding cavity is almost completely hydrophobic except for a hydrogen-bonded network formed by three water molecules, the backbone of residues 300 302, and the flavin ribityl, similar to P293, and three crystal waters in para-hydroxybenzoate hydroxylase suggest that P302, T47, and the waters in StyA are a vital component of the catalytic mechanism.
This loop, which constitutes a flap closing the binding cavity, is locked by the third coordination bond established between His57 and Fe2+ (Figure 2A).
Although the sequences have structures that exhibit a 3/3 Mb fold, the heme binding cavity is defective due to the pulling apart of helical strands.
The ligand binding cavity is situated between the β-sheet and the helix.
The engineered binding cavity is known to be polar, solvated and deeply buried.
In the case of the L. lactis OppA, the binding cavity is exceptionally large.
Unlike other LRR proteins, the ligand binding cavity is located in the convex region, which lies in between LRR9∼12 [31].
The binding cavity is L-shaped with similarities to honeybee PBP [28] the wider part being towards the rim of the entrance.
The comparison of the volume of the ligand binding cavity is 418 and 503 Å3 and the retinoic acid occupies 66.5 % and 55.3 of the pockets for RARα and RARα, respectively.
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CEO of Professional Science Editing for Scientists @ prosciediting.com