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. In some cases there is minor heterogeneity among subunits caused by posttranslational modifications, point mutations, or micro-heterogeneity. In the stoichiometry calculation minor differences among subunits are ignored: if the sequence identity is >= 95% over 90% of the sequence length of two protein chains, they are considered identical. Protein chains with less than 24 residues, nucleic acid chains, and ligands are ignored.
By default, a 95% sequence identity threshold is used for the stoichiometry assignments. In addition, stoichiometry is calculated at 30% sequence identity. If we consider hemoglobin again, at 95% sequence identity threshold the alpha and beta subunits are considered different, which correspond to an A2B2 stoichiometry. At the 30% sequence identity level, all four chains would be considered homologous (~45% sequence identity) with an A4 pseudostoichiometry.
A2BCD with Stoichiometry (95% Sequence ID): finds protein complexes with 2 alpha, 1 beta, 1 gamma, and 1 delta subunit, for example the acetylcholine receptor PDB ID 4AQ5.
A5 with Pseudostoichiometry (30% Sequence ID): finds protein complexes that are homopentamers at 30% sequence identity threshold. This search returns for example PDB ID 4AQ5, which is an acetylcholine receptor with 2 alpha, 1 beta, 1 gamma, and 1 delta subunit because these subunits are homologous at a 30% sequence identity threshold.