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Quite simply, a flavoprotein is a protein which contains a flavin cofactor either covalently or noncovalently bound to it. Approximately 95% of the flavoproteins currently in the PDB are enzymes of one sort or another. In the remaining 5% the flavin is said to be a structural support, although when pressed most biochemists will admit that they're probably enzymes, it's just that nobody has yet figured out which reaction it is that they catalyze.

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