Thanks for the report - we also discovered this issue at the same time. I have a fix which should go live later today. (It is a result of the RCSB PDB changing the URLs for the file downloads)
Also, if you are using the PDBConnector, please be aware of our post yesterday at https://tech.knime.org/forum/cheminformatics/changes-to-rcsb-pdb-queries.
We have just uploaded the newly correct version to the nightly build and to the stable builds for version 3.3 and 3.2.
On consequence is that we have just deprecated the current form of these nodes (although they do now work again!), and replaced them with new versions which also allow downloading NMR Shifts and restraints for those structures where that is relevant.
I will put up a new post imminently dealing with the changes....