What is meant by “unique ligand” on the RCSB Protein Data Bank website?

Question

I went to the https://www.rcsb.org/ site, and searched for some proteins. For each entry, “unique ligands” are listed.

I understand a ligand is a molecule or ion that binds to a metal atom. I don’t understand what a unique ligand is. Why is this important? What can we do with this information?

Answer 1

Your understanding is incorrect. A ligand at its most basic is a molecule that binds to another molecule. There is no requirement for metal atoms whatsoever. In the context of RCSB (home of the Protein Data Bank) we are only concerned with ligands that bind to macromolecules, the structures of which are presented there — usually proteins. The following definition is in the Glossary on the RCSB site.

ligand - A molecule that binds specifically to another molecule (usually a protein or nucleic acid) to form a complex. A ligand can be another protein, but is often a small molecule.

I’ll assume a protein here.

Original Answer

Unfortunately that Glossary doesn’t explain their usage of “unique” in this context, perhaps because it may be a recent modification. However what it would appear to me to be is an aid to distinguishing those molecules that bind in a biologically significant manner to a protein, from those molecules — metal ions and molecules like glycerol — that only bind to the protein because they are present at a high concentration in the crystallization or other preparation medium. Such molecules are likely to be present in more than one copy, i.e. not unique.

Why not just say “biological ligand” rather than “unique ligand”? The fact that only a single molecule is present doesn’t prove it is biologically significant, and this information would seem generally to be absent from submission information (in my experience). The job of the curators of PDB is to describe rather than interpret.

Edit: 17 June 2021

After inspecting several entries it became evident that my original interpretation of “unique ligand” as “individual ligand” (with a suggestion of biological relevance is incorrect. There are examples of non-biological molecules, molecules present several times, and molecules occurring in different numbers in different identical subunits all listed as “unique ligands” (@canadianer also commented on this.) The bromide ions in protein 2RC3.pdb provides an example.

I wrote to support at RCSB Protein Data Bank and I would summarize the situation as:

Any non-polymer, non-water molecule in the structure is designated in the RCSB interface (but not in the mmCIF data format) as a “unique ligand”.

The support at RCSB tacitly acknowledged the unsatisfactory nature of this and stated in their reply that “We will re-visit the use of this term.”.

As the reply was from support, I feel that it is reasonable to quote from it, but thought it better to exclude the name of the actual contact.

In short, “unique ligand” means: each of the distinct small molecule entities present in the PDB entry (i.e. a “non-polymer entity” in mmCIF nomenclature).
The word “unique” is our attempt to describe what an entity means in a brief way.  We will re-visit the use of this term.
Please note that the data is very well described in mmCIF format (https://mmcif.wwpdb.org/; https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_entity.id.html).
For example, here is an excerpt of the mmCIF file for the 2RC3 entry:
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer     man 'CBS domain'                      15169.631 4   ? ? ? ? 
2 non-polymer syn 'BROMIDE ION'                     79.904    39  ? ? ? ? 
3 non-polymer syn NICOTINAMIDE-ADENINE-DINUCLEOTIDE 663.425   4   ? ? ? ? 
4 water       nat water                             18.015    710 ? ? ? ? 
Lines 12 and 13 correspond to the 2 “unique ligands” shown on the structure summary page.

and then is a second message:

To clarify, entity is a chemically distinct part of an mmCIF entry.
For example, looking at entry 4hhb (https://www.rcsb.org/structure/4HHB), there are 2 "unique" protein chains OR 2 protein entities.  There are 2 copies of the alpha subunit (chains A and C; one entity) and 2 copies of the beta subunit (chains B and D; a second entity).