We are currently working on getting a web server online which will make Protein Ligand Graphs for the whole PDB available.
At this time, you can already download the graphs for 151,633 protein chains from the PDB in a ZIP archive.
The graphs in the archive are the albelig graphs, i.e., the full protein graphs considering helices, beta strands and ligands. They were generated using a shell script with PLCC version 0.67, using the following command line options:
--dont-write-images --sse-graphtypes f --outputformats ge -k -K
You can download the graphs in Graph Modeling Language (GML) or Kavosh Edge List format below:
NOTE: The ZIP archive contains the graphs in a PDB-style directory tree, i.e., you will find graphs for PDB protein 8ICD under the path /ic/8icd/, just like on the PDB FTP server (having > 100,000 files in a single directory hurts most file system browsers).
You should also keep in mind that these graphs most likely contain lots of redundancy (e.g., many graphs of hemoglobin because there are many crystal structures of hemoglobin in the PDB).