Protein Symmetry

Search for protein complexes with a given symmetry

Protein symmetry refers to point group or helical symmetry of identical subunits (>= 95% sequence identity over 90% of the length of two proteins). While a single protein chain with L-amino acids cannot be symmetric (point group C1), protein complexes with quaternary structure can have rotational and helical symmetry:

Symmetry

Complexes are considered symmetric if identical subunits superpose with their symmetry related copies within <= 7 Å Cα RMSD. 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. The symmetry information is calculated for the first biological assembly, if available. Otherwise, it is determined from the PDB entry itself.

Examples:

C5 finds protein complexes with C5 symmetry

H finds helical protein complexes