Here you may download at once all PDB files used in the 3DComplex hierarchy (The archive is 18Go!). These are the PDB Biological Units as of March 1st 2017, modified in the following way:
And here are the Updated assemblies (2022)
- The ATOMIC residues have all been renumbered according to the SEQRES sequences. (Sometimes the residue numbering in PDB files can be wrong for various reasons)
- The chains have been renamed sequencially so that there is no double. (In the PDB Biological Units, duplicated chains carry the same name)
For this reason, you may need the correspondancy file, which provides the mapping between duplicated chain names and original chain names.
You might also need the fasta file of the SEQRES sequences.
Here you can download a file giving the contacts between chains for all structures . Information contained in the file is detailed below:
- code : pdb code
- ch1 : chain identifier 1
- ch2 : chain identifier 2
- nres : number of residues in contact
- len1 : length of chain 1
- len2 : length of chain 2
- dom_s1 : domain architecture of chain 1 as defined in SCOP
- dom_p1 : domain architecture of chain 1 as defined in PFAM
- dom_s2 : domain architecture of chain 2 as defined in SCOP
- dom_p2 : domain architecture of chain 2 as defined in PFAM
- ident : whether the two chains are identical (0/1)
- homo : whether the two chains are homologous (0/1)
Below you can download the hierarchy:
- Each List link points to the list of representative complexes at each level.
- Each Clusters link points to the clusters of complexes found at each level. Note that at the topological level, this can be useful to retrieve, for instance, all dimers at once.
- The graph images for all complexes can also be downloaded: full graphs, or topology only.
| Top-down Hierarchy (Type 1, see Help for details) | Bottom-up Hierarchy (Type 2, see Help for details) |
|
| QS Topology level | List - Clusters | List - Clusters |
| QS Family level | List - Clusters | List - Clusters |
| QS level | List - Clusters | List - Clusters |
| QS20 level | List - Clusters | List - Clusters |
| QS30 level | List - Clusters | List - Clusters |
| QS40 level | List - Clusters | List - Clusters |
| QS50 level | List - Clusters | List - Clusters |
| QS60 level | List - Clusters | List - Clusters |
| QS70 level | List - Clusters | List - Clusters |
| QS80 level | List - Clusters | List - Clusters |
| QS90 level | List - Clusters | List - Clusters |
| QS100 level | List - Clusters | List - Clusters |
| All proteins | List | List |