We have become aware of problems with some query types in the PDB Connector nodes since a backwards-incompatible change to the RESTful API hosted by www.rcsb.org in the last week or two.
We are currently working on an update to the PDB Connector Query Builder node, but it is not clear at the moment how difficult that might be, or whether we will be able to transfer existing affected queries.
As an update, version 1.30.3 of our community contribution fixes this without breaking existing queries. It is currently available in the stable release channels for KNIME 4.1, 4.2 and 4.3. hopefully it will be available on the 4.4 stable release and trunk by the end of next week.