Many proteins normally exist as oligomers, but the oligomer is
in the published PDB file. An educated guess about the
complete oligomer, and the corresponding PDB file, is available at the
Probable Quaternary Structures (PQS) site of the European
In order for PQS to report a specific oligomer, that oligomer must occur in the
crystal, or else the authors of the PDB file must specify the symmetry
operations required to generate the oligomer (commonly done for virus
capsids). PQS looks at the interchain contact patches in the crystal, and
makes an automated judgement about whether they are likely to represent
specific oligomer interfaces, or merely contacts that occur only in the
(Henrick & Thornton, 1998).
Any contact less than 400 Å2 per chain is deemed a
The mean area of specific contact between a protein antigen and an antibody
is 800 Å2 per chain
In order to be deemed a
specific oligomeric contact by PQS, the contact must not only have an
interfacial area larger than 400 Å2 per chain,
but must also satisfy
an empirical weighted score with contributions from the loss of solvent
accessible surface, gain in solvation free energy,
the number of residues buried at the interface, and the
number of salt bridges and disulfide bridges, if any.
There are numerous possibile relations between the asymmetric unit
in the published PDB file, and specific oligomers. Here are some examples.
Another example is
The specific oligomer is a hexamer, but file 5cev contains two half-hexamers
with a crystal contact interface between them.