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Other proteins and peptides, i.e., oligo- and polypeptides of any amino acids chain length
Nucleic acids (DNA or RNA)
Peptides, i.e., oligopeptides with less than 20 amino acids in length
Small molecule drugs, agonists, substrates, substrate-competitive inhibitors but not cofactors
Cofactors and ligands that overlap with cofactors, e.g., cofactor-competitive inhibitors
Covalently attached O- and N-glycans
Conserved water molecules, i.e., those found in more than 10 PDB structures (num_occ > 10) at the same location and having high conservation score (cons > 0.6)
Biologically relevant metal ions, i.e., those found in more than 10 PDB structures at the same location