Questions on Antibody Structure
by Eric Martz, October 1997; revised January 2001

Many of these questions can be answered by referring to the images at It will also be helpful to refer to the appropriate chapter of a textbook of immunology.

These questions will help you focus your tour of antibody structure. It is recommended that you print this page and write your answers. Before leaving class today, have your answers checked by your instructor.

For those interested in learning more about protein structure visualization, Protein Explorer is easy-to-use freeware you can use on your computer. You can look at cytokines, MHC, TCR, CD4, HIV gp120, etc. Instructions, with links to those molecules, are at the end of this document.

    Ig Domain

  1. How many beta sheets are there in an Ig domain? How many beta strands are there in each sheet?

  2. Are adjacent beta strands (in the sheets) parallel or antiparallel? (In the cartoon representation, the arrow begins at the amino N-terminus of the strand, and points to the carboxy C-terminus [arrowhead].)

  3. What two types of bonds are largely responsible for holding the two sheets together?


  4. What kinds of bonds hold the heavy chain fragment to the light chain fragment in the Fab?

  5. What kinds of bonds hold the antigen (lysozyme) to the antibody?

  6. How many CDR's are there in the paratope? (The paratope is the site on Ab to which the Ag epitope binds.)

  7. Draw a map of the paratope showing the relative positions of the CDR's.

  8. Which CDR's are most variable? Where do these CDR's lie in the paratope?

  9. How many of the epitope-contact atoms in the paratope are not in the CDR's?

  10. How many amino acids of lysozyme are in contact with the Fab? How many separate blocks of sequential amino acids are in the epitope?

  11. Do all (or most) of the CDR's contact the epitope?

  12. There appears to be a hole in the middle of the spacefilled Fab. In reality, what would fill this hole?


  13. What holds together the two arms of F(ab')2?

  14. Are the two light chains covalently linked to each other with disulfide bonds? The two heavy chains?

  15. What are the light chains covalently linked to?

  16. Where are the majority of disulfide bonds in IgG, and what do they link together?

    Whole IgG

  17. How many polypeptide chains make up an IgG molecule?

  18. Which domains have carbohydrate attached? How might this carbohydrate contribute to the function of these domains?

  19. What is the function of the thinnest part of the IgG molecule?

  20. What important feature of antibody function is not visible in these images?

  21. What kind of chemical bond does pepsin break when it makes F(ab')2?

    Comparisons between moieties

  22. How many immunoglobulin domains are there:

    1. In IgG?

    2. In F(ab')2?

    3. In Fc?

    4. In Fab?

    5. In Fv?

  23. How many variable domains are there in each of the above structures?

  24. In IgG, how many pairs of Ig domains are there? How many of these pairs are not directly attached to each other, side to side? Why aren't they?

  25. SDS PAGE separates proteins according to their molecular weights. The molecular weight of IgG is 150,000 Daltons. What is the molecular weight of:
    1. a single immunoglobulin domain?
    2. Fab?
    3. F(ab'2)?
    4. Fc?

  26. Can Fc be clearly resolved from Fab by SDS PAGE?

  27. What are the approximate dimensions of a single Ig domain? (Hint: use the distance reporting mode available from the utility menu. It reports in Angstroms.) What about the nose-to-tail distance for a whole IgG molecule?

  28. What is the approximate size of a protein epitope? (Measure the largest distance between contact atoms in the CDR's.)

  29. A lymphocyte is about 10 micrometers in diameter. How many Angstroms is this? What is the approximate ratio of the diameter of a B lymphocyte to the diameter of its Ig receptor?

End of questions.

Optional: Protein Explorer

  1. Protein Explorer is freeware that makes it easy for you to look at the structure of any protein for which a structure has been published. Protein structures cannot be accurately predicted from amino acid sequence. They are determined experimentally by X-ray crystallography, or sometimes by nuclear magnetic resonance (NMR). Structures have been published for several thousand different proteins, and many mutated proteins. All published macromolecular structures are available from the Protein Data Bank (PDB).

  2. If you go to this page on the web, you can click on the following hyperlinks. Go to

  3. The Fab:lysozyme structure used in the above tutorial is 1FDL. The FirstView page in Protein Explorer explains the view of 1FDL it shows you initially. Then, click on Explore More, and you will go to the QuickViews menu page, where you can try these:

  4. Other molecules of interest:

  5. Want to look at something besides antibody? The easiest place to find a protein structure, using the name of the protein, is at PDB Lite (

  6. Once you find a protein, note its 4-character PDB identification code. Then go to Protein Explorer ( and enter the code in the slot at the FrontDoor.

Feedback to Eric Martz.