What is in the PDB gene association file?
The PDB file is made differently from the UniProtKB-GOA UniProt gene association file. PDB entries are only assigned GO terms based on matches between PDB entries and InterPro domains. This file no longer contains annotations from sources where GO terms have been assigned to entire UniProt protein accessions (i.e. from GOA:manual, GOA:SPKW, GOA:SPEC or GOA:HAMAP sources). This change has been made to avoid assigning GO terms to PDB chains where some terms might only be correct for the corresponding whole protein. InterPro2GO (SCOP and Cath) signatures and PDB chains are superimposed on the UniProtKB protein and if there is a good overlap then the InterPro mapping is produced. This data is provided by the InterPro3D group at the EBI. In future we intend to supplement this data by including manual protein binding annotations via the IntAct protein-protein interaction database.
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