What happens to the rest of the 95 percent in quarks? Quarks are bound by gluons. Gluons have a mass of 0, while mass of quarks is only 5%.
Where is the missing 95%?
 A: It's tied up in the energy of the interaction, which "looks like" mass.
A: In the level of quarks and gluons one is in the realm of quantum mechanics and special relativity. Special relativity assigns to each particle a four vector , whose "length" is the invariant mass of the particle .


The length of this 4-vector is the rest energy of the particle. The invariance is associated with the fact that the rest mass is the same in any inertial frame of reference.

Thus all particles are of fixed mass, but mass is not an additive quantity, in the same way that in three vectors the length  of the new vector from the addition of   two vectors is variable. Thus the rest of the mass of the proton comes from the added four vectors of the multitude of quarks antiquarks and gluons. See this.

This is a rough argument, as quantum mechanics has to be involved,
, and the  the particles in the picture are off mass shell, and one needs a theory to get the bound proton, as lattice QCD, but the four vector algebra is true and gives a feeling for how although zero mass and low mass particles can compose the proton.
