Rhodopsin

The interesting thing about retinal is its photochemistry. I will talk about that soon. But this is another one of the protein-with-functional-group-picture posts. I still haven't quite realized how nice PyMOL is and I still enjoy making pictures with it. But of course also thanks to Röntgen and Bragg. And Edwards et al. who investigated the structure of this bovine rhodopsin.

This is the subunit with retinal (shown in red). Long stretched helices.

Retinal is bonded to a lysine residue (pink) to form an iminium ion. Or protonated Schiff base as they say if they are trying to confuse me. Retinal fits nicely into the helices. The π-system is almost planar only the double bond in the ring kind of sticks out. The 11-cis-bond (where I don't understand why it is called 11, probably a terpene nomenclature) is behind the green arc.

Carboxylic groups surrounding retinal are important for the charge distribution. You can select them in PyMOL with the following command (after making a selection "retinal" with retinal):

select SurrAc, (retinal around 10) and resn asp+glu

There is one at the iminium group ...

... and one at the β-ionone ring.

They give the molecule kind of a jungle feeling.