At RCSB PDB we are currently working on an all vs. all comparison of PDB. A preliminary version of this is available from the betastaging site for public testing. e.g.:
This is a beta site so it might not always be available or some things might not work as expected, still it should give you a pretty good impression of what is in preparation. If you want to help testing, have a look there and let me know how it goes.
Some documentation on the all vs. all procedure can be found here: