Here we see a representation of a complete antibody, consisting of four distinct polypeptide chains: two "light chains" (green and blue) and two "heavy chains" (red and yellow). The ball-and-stick representation showing all atoms and bonds is once again very confusing, and switching to a backbone view allows us to see the course of the polypeptide chains more clearly:
In this view, we clearly see how each chain contains separate compact regions (two for the light chains, four for the heavy chains), which are connected by short, more extended regions. These compact regions are called domains.
It is clear that proteins are built on a larger scale than smaller organic molecules than the familiar sucrose molecule (which is shown next to it for scale). We can also see that the length of the folded protein chains still runs in the tens of nanometers:
Also note that the antibody itself carries a number of covalently attached carbohydrate residues, in between the two heavy chains. These glycans are added to the polypeptide chain and modify the physicochemical properties of the whole molecule. They can for instance increase the solubility of the protein. Many macromolecules combine properties of different chemical classes.
The four separate polypeptide chains are held together in part by a number of disulfide bridges, formed by the formation of a covalent bond between two cysteine side chain sulfhydryl groups:
Each domain has one internal disulfide bridge (yellow). The two heavy chains are linked by three bridges (orange), and the each light chain is also linked to its partner heavy chain by a single bridge (blue).
The defining characteristic of an antibody is its
ability to specifically recognize and bind to another
molecule, which is called the antigen. In larger antigens
the antibody generally recognizes only a limited region,
which is called the epitope. The part of the antibody
that directly interacts with the epitope, and determines
the specificity of the interaction, is called the paratope.
The paratope is formed by a number of superficial loops
in the N-terminal domains of the heavy and light chains: