At most that will allow the OP to read his data files.
Well, it was also meant for others, and as a hint to the OP. Whatever the precise question; it is useful to know if a widely used format is being discussed. Taking myself as example: to realise that this data is PDB (I had to look up the format at the PDB site) got *me* interested -- and perhaps I'll give it a try with postgres/postgis later on (I think there is actually quite a bit of 3d stuff available between them).
The advantage would mainly be indexing, I think, so if a database approach can be made to work at all, it would mostly be useful if one wanted to look at many proteins.