Ligand Serial Number

[gcyoung]

How is the Ligand Serial Number column created? I want to be able to extract the bound ligand from the pdb structure based on the information available in the BioLip TSV. I know I can download the ligand from BioLip as well but I'd prefer not to have to download additional structures if possible. If I can know how the Ligand Serial Numbers are assigned, then I can use that information to figure out which ligands they correspond to in the pdb structure.

[zcx@umich.edu]

To differentiate different ligands of the same type in the same chain, the tsv file offers at column 7 the Ligand serial number. For example, PDB 117e chain A (https://zhanggroup.org/BioLiP/qsearch.c ... 7e&chain=A) has three MN and two PO4. The first 7 columns of the corresponding tsv reads:
117e A 2.15 BS01 MN A 1
117e A 2.15 BS02 MN A 2
117e A 2.15 BS03 MN A 3
117e A 2.15 BS04 PO4 A 1
117e A 2.15 BS05 PO4 A 2
For example, the last row column 7 reads "2" because it is the second PO4 in the chain.

[gcyoung]

Thanks for the response! However, I'm still confused. I understand that the Ligand Serial Number can tell us the "index" of the ligand in the mmCIF file for that chain, ie Ligand Serial Number 2 would mean it's the second ligand mentioned in that chain with that name. I'm still confused how I can use that information to access that specific ligand when I load the mmcif file into a structure object with eg schrodinger.StructureReader or BioPython. Can you help me with that?

[zcx@umich.edu]

If your purpose is to load the structure of the ligand, you can directly batch download all ligand structure from
https://zhanggroup.org/BioLiP/weekly.html
If you only need one specific ligand in a structure of your interest, you can download it from the "[Download ligand structure]" link in the ligand-protein interaction page, e.g., https://zhanggroup.org/BioLiP/pdb.cgi?p ... =B&bs=BS01

[gcyoung]

I actually need access to the atoms of the bound ligand within the pdb file, rather than just a separate file containing just the ligand. Is there a way to do that?

[zcx@umich.edu]

I have just updated the BioLiP web interface to add the residue information. For example, at https://zhanggroup.org/BioLiP2/pdb.cgi? ... =G&bs=BS01
the "Ligand information" says "8gwo Chain A Residue 1003" where 1003 is the residue sequence number (_atom_site.auth_seq_id in mmCIF file). I am working on the update code to include this as an additional column in the BioLiP tsv file, which should be updated by next week.

[zcx@umich.edu]

I have updated the tsv file to include the residue sequence number as the last but one column in BioLiP.txt.

[gcyoung]

Wow, thank you! That's very helpful and will save you a lot of API requests.

[gcyoung]

Hi,
Following up on this, it looks like some of the ligand residue numbers have letters in them e.g. 479G.

[zcx@umich.edu]

This is not a bug. Some ligand residue numbers have insertion code (https://proteopedia.org/wiki/index.php/ ... tion_Codes). In your example, 479G means the ligand is residue 419 with insertion code G.