Missing residues and incomplete sidechains

From Proteopedia

Missing Residues

In about 90% of the Empirical models in the PDB, some residues (amino acids or nucleotides) that were present in the experimental material are absent (have no coordinates) in the empirical model. X-ray crystallography gives a clear electron density map only where every molecule in the protein crystal has the same conformation. Usually, some parts of the molecule vary in conformation between copies in the crystal, that is, some regions are disordered. The same may occur with protein molecules on a cryo-electron microscopy grid. These disordered portions of the molecule are not clearly resolved in the density map used to construct the structure model. Without density to guide where to place these residues, the experimenter omits them from the model. These are called missing residues. It is very common for a few residues at the ends of protein chains to be missing in the atomic model. (Example: 5 residues are missing from the carboxy terminus of the protein in 1ijw.)

To emphasize, the missing residues were present in the experimental material, but are absent in the resulting atomic model.

Missing Ends of Chains

Unlike other viewers, FirstGlance in Jmol ensures that you are aware of missing ends by marking them with spherical "empty baskets" (see #below). In the example shown below, 2ace, the 3 missing N-terminal residues DDH have net negative charge.

Missing Loops

FirstGlance ensures that you are aware of missing loops with an ellipsoidal "empty basket". Other viewers us a less obvious dotted line.

Incomplete Sidechains

In about 70% of the Empirical models in the PDB, some residues have coordinates missing for some of the atoms in their sidechains, due to local disorder. But their main chain atoms are present in the model, leading to residues with incomplete sidechains. For example, the long sidechain of a lysine on the surface of a protein may have too blurry an electron density to indicate its position. In some cases, the model builder may give that sidechain coordinates with high temperatures, or low or zero occupancy. In other cases, the model builder simply omits the coordinates for the sidechain, so the aforementioned surface lysine may have the sidechain of an alanine (example: Lys498 in 2ace).

How to avoid overlooking missing residues or incomplete sidechains

When a PDB ID model is displayed in FirstGlance in Jmol, regions with missing residues are clearly marked with "empty baskets", as shown at right. FirstGlance reports the total number missing, and the resulting number of missing charges.