Protein Stoichiometry

Search for protein complexes with a given stoichiometry

The stoichiometry of a protein complex represents the composition of its subunits. For example, the biological assembly of hemoglobin has two alpha and two beta subunits, represented by the stoichiometry formula A2B2. Protein subunits are considered identical if their pairwise sequence identity is >= 95% over 90% of the length of both sequences, to account for minor sequence variations such as point mutations and truncated or disordered N- and C-terminal segments. Protein chains with less than 20 residues are excluded, unless at least half of the chains are shorter than 20 residues. Nucleic acids and carbohydrate chains, as well as ligands are excluded.Split entries (entries divided between multiple coordinate files due to the limitations of the PDB file format) are currently excluded from the protein stoichiometry and protein symmetry features. Stoichiometry is calculated for the first biological assembly, if available. Otherwise, it is determined from the PDB entry itself.

Protein stoichiometry is specified by a composition formula. Each type of different protein is assigned an UPPERCASE letter A, B, C ... in alphabetical order. These letters do not represent chain identifiers. The number of equivalent subunits is added as a coefficient after each letter. For example, a hetero-trimer with 2 identical subunits, and one different subunit is specified as A2B. Larger coefficients must be specified first, for example, AB2 is not a valid specification, but A2B is valid.

BELOW: Hemoglobin with 2 alpha and 2 beta subunits (Stoichiometry A2B2). Read more information about protein stoichiometry and symmetry.

symmetry mode

Examples:

A5 finds all homo-pentameric protein complexes

A2B2 finds all dimers of dimers, i.e., hemoglobins