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I think you've got that last part backwards. When you have constituents with binding energy, that reduces the total energy of the system and reduces the mass. So it seems that the mass of the proton is quark mass + gluon kinetic energy - bonding energy, and most of the mass comes from gluon kinetic energy.

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Thank you.

Would like to understand that why does having constituents with binding energy reduce the total energy of the system instead of adding to it?

You have to think about it the other way around: The constituents don't have binding energy. That energy becomes available when you let them bind, and you have to pay it back if you want to unbind them.

Example: If you have a proton and an electron, making a hydrogen atom will release about 13.6 eV (if it goes to the lowest energy state). You have to spend that 13.6eV to ionize the hydrogen, i.e. to get the electron far away from the proton again.

Yes I do indeed; thank you for the correction!

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