Each dataset is represented using two files: one to map the UniProt IDs to corresponding PDB IDs and the second that provides annotations of binding for these PDB IDs.

The file with the suffix '.UniprotPDB' is the mapping of protein IDs between UniProt and PDB. Each line in this file includes one protein which is represented using multiple columns:
- The first column is the UniProt ID
- The following multiple columns are the PDB IDs of chains that were mapped into this Uniprot ID together with annotation of the type of binding that they cover

The file with the suffix '.annotations' includes mapping of pdb chains into each of the uniprot sequence. For each uniprot sequence, we include all PDB IDs with the corresponding annotations from the source PDB chains. Each PDB ID is associated with its corresponding type of binding and may include multiple annotations that correspond to multiple source PDB chains. Each pdb chain is described using three lines:
- The first line shows pdb ID and the chain number
- The second line includes the pdb sequence where . represents a residue that is not present in the PDB chain but is present in the UniProt sequence (inclusion of . is to align this PDB chain to the corresponding UniProt sequence)
- The third line is the annotations of binding residues where the letter indicates the binding residues