Apo structures for protein-ligand complexes in PDBbind V. 2019
Data download link : https://pitt-my.sharepoint.com/:f:/g/personal/ria43_pitt_edu/EtwrtGBrS49MuezZtoxRQ3UBoJTHvPPGh8IV3JjzPpT91A?e=Asx29i
You'd find that the folders with apo structures would have the following files:
*_protein.pdb - the original holo protein structure
*_apo.pdb - apo protein structure
*_apo_added.pdb - apo protein structure with missing residues added
*_protein_nowat.pdb - holo protein structure with water molecules removed
*_ligand.sdf - crystal pose structure of the ligand
There's also "apobind_all.csv" that contains more information about apo-holo pairs in the dataset.