PDB is an important data archive for protein structures and their structural information. Majority of structures available are obtained from X-ray crystallography. PDB file contains the coordinate information of the atoms including their spatial organisation. The water molecules are represented as HETATM (heteroatoms to the primary structure), which denotes the atoms that are not primary to the structure of the protein, i.e. non-main chain atoms.

How are water molecules symbolised in PDB files that contain coordinate information?

In a PDB file, the water atom is represented as ‘HOH’ that symbolises its arrangement of atoms. In crystallisation, water exists as water of crystallisation, where water is added to the protein to stabilise the crystal. Proteins are charged molecules and are localised in the cell where water is the solvent. So, in order to maintain its folded structure, water forms hydrogen bonds and therefore, water is added to stabilise the structure outside of the cell. During simulation process, the water which acts as a solvent, can be removed but the water molecules present as water of crystallisation cannot be removed.