Time for some more graphics. I picked GFP which is not really a new idea but it is a pretty cool molecule.
In the sphere model all proteins pretty much look alike. But I still think kind of cool, especially if you use Lightnir's QuteMol preset for pymol.
The cartoon model shows you more about the structure. GFP consists of a β-sheet "barrel" that encapsulates the chromophore. You need a rigid structure if you want to make sure that the chromophore does not quench before it is able to show fluorescence. It is interesting to compare this to Rhodopsin which is apparently much more flexible. This makes sense since in Rhodopsin the biological activity is related to non-radiative decay and isomerisation.
The chromophore is trapped at the center of the barrel.
Interestingly the chromophore is made directly out of amino acids. You can take a look at it and think of how this is done.
The answer is here. The hydroxyphenyl comes from tyrosine (as expected). The imidazolon ring is formed after cyclization, the bridging double bond through oxidation. It is interesting to consider that this apparently works in many different organisms and not just in the jelly fish aequoria victoria. The driving force seems to be that the amino acids are pressed together in the barrel.
The chromophore is part of the protein chain. It is connected to the helix that goes through the center of the protein.
Or from a different perspective.