Missing residues and incomplete sidechains
From Proteopedia
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To emphasize, the missing residues were '''present''' in the experimental material, but are '''absent''' in the resulting model. | To emphasize, the missing residues were '''present''' in the experimental material, but are '''absent''' in the resulting model. | ||
| - | + | ==Incomplete Sidechains== | |
| - | In less extreme cases, the sidechain of an amino acid may be missing due to disorder, but its main chain atoms are present in the model, leading to ''incomplete sidechains''. For example, the long sidechain of a lysine on the surface of a protein may have too blurry an electron density to | + | In less extreme cases, the sidechain of an amino acid may be missing due to disorder, but its main chain atoms are present in the model, leading to ''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 low or zero [[occupancy]]. In other cases, the model builder simply omits the coordinates for the sidechain, so the aforementioned surface lysine may be modeled as alanine. |
Revision as of 17:22, 29 October 2024
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. Local regions of the crystal (for X-ray crystallography), or of the molecules prepared for cryo-electron microscopy, which were disordered 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.
To emphasize, the missing residues were present in the experimental material, but are absent in the resulting model.
Incomplete Sidechains
In less extreme cases, the sidechain of an amino acid may be missing due to disorder, but its main chain atoms are present in the model, leading to 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 low or zero occupancy. In other cases, the model builder simply omits the coordinates for the sidechain, so the aforementioned surface lysine may be modeled as alanine.
