NOTE: Most of these structure files are derived from crystallographic structures of proteins carrying these molecules. In most cases, crystallographic images are not sharp enough to reveal hydrogen atoms. Therefore, hydrogens are missing from most of these files. A biochemist’s knowledge of organic chemistry tells her or him where the hydrogens are located. You will quickly become accustomed to seeing biological structures without the hydrogens. (The title of this section is Nucleotide Coenzymes. Which of the following are better described as coenzymes, cofactors, cosubstrates, or prosthetic groups?)
Often 1 pdb file can also contain a series of different structures / inhibitors etc for the same protein system.
In this pdb we see that waters #187 and #183 form a disordered pair and so both should not be present. Thus I will arbitrarily remove water 187 from the pdb file and keep 183. I will also remove all of the connectivity data at the end of the PDB as this will not be used by XLeap.