3D Complex: A Structural Classification of Protein Complexes
Figure 3
Examples of Quaternary Structure Topologies
(A) All QSTs for complexes with up to nine subunits are shown, accounting for more than 96% of the nonredundant set of QSs and more than 98% of all complexes in PDB. Topologies compatible with a symmetrical complex are annotated with an s, and topologies where all subunits have the same number of interfaces (edges) are annotated by a star (*).
(B) Examples of large complexes that are the single representatives of their respective topologies (QSTs). PDB codes are given. 1pf9, E. coli GroEL-GroES-ADP; 1eaf, synthetic construct, pyruvate dehydrogenase; 1shs, Methanococcus jannaschii small heat shock protein; 1b5s, Bacillus stearothermophilus dihydrolipoyl transacetylase; 1j2q, Archaeoglobus fulgidus 20S protesome alpha ring. It is interesting to note that the graph layouts resemble the spatial arrangements of the subunits.
(C) Likely errors in the PDB Biological Units: QSTs of homomers with different numbers of contacts amongst the subunits. The number of erroneous QSs in each topology is provided above each graph.