BioLip column names clarification

[zy417]

Hello,
Thanks for your great work on the BioLip database!

In the dataset I downloaded from your website, there are two columns: “Binding Site Number Code” and “Ligand serial number”. After reading the descriptions provided for the two columns, I’m still not sure what they are referring to. Could you briefly explain to me what they mean and how they are collected?

Thank you!

[zcx@umich.edu]

Residue sequence number (i.e., column 23 - 26 in PDB format file or _atom_site.auth_seq_id in mmCIF format).

[zcx@umich.edu]

“Binding Site Number Code” is the index of ligand binding sites. For example, PDB 10mh chain A has three ligands: two DNAs and one SAH. Their binding sites are sequentially numbered BS01, BS02, BS03, respectively.

[zy417]

For your response regarding "Ligand serial number":

I think you are referring to the "Residue sequence number of the ligand (field _atom_site.auth_seq_id in PDBx/mmCIF format)" in the readme file provided from your website (https://zhanggroup.org/BioLiP/download/readme.txt) but not the one that I was asking about.

Would you mind clarifying what "Ligand serial number" means?
Thank you!

[zy417]

For the Binding Site Number Code, I am still a bit confused.
When I look at pdb 2y41 (below is part of the pdb information of the ligands), chain A has 2 ligands(IPM and MN), chain B has 4 ligands(IPM,MN,MN,MN).
These I suppose that they should have the following binding site number code: Chain A (BS01:IPM, BS02:MN) Chain B (BS01:IPM, BS02:MN, BS03:MN, BS04:MN).
However, in the dataset I downloaded, for the entries in 2y41, chain B has MN as BS03 and also has IPM as BS03. Why would they have the same binding site number code? Shouldn't IPM be BS01?
Is my understanding incorrect?
Thanks a lot in advance!





HETATM 5228 C1 IPM A 800 -8.336 -35.712 18.102 1.00 31.17 C
HETATM 5229 C2 IPM A 800 -9.274 -36.048 16.970 1.00 32.89 C
HETATM 5230 C3 IPM A 800 -8.570 -35.676 15.623 1.00 32.60 C
HETATM 5231 C4 IPM A 800 -7.191 -36.353 15.485 1.00 34.28 C
HETATM 5232 C5 IPM A 800 -9.472 -35.858 14.385 1.00 35.42 C
HETATM 5233 C6 IPM A 800 -8.696 -35.458 13.121 1.00 30.32 C
HETATM 5234 C7 IPM A 800 -10.790 -35.054 14.488 1.00 30.02 C
HETATM 5235 O1 IPM A 800 -9.527 -37.439 16.946 1.00 33.32 O
HETATM 5236 O2 IPM A 800 -7.792 -36.625 18.657 1.00 32.47 O
HETATM 5237 O3 IPM A 800 -8.044 -34.426 18.286 1.00 32.02 O
HETATM 5238 O4 IPM A 800 -6.115 -35.663 15.918 1.00 30.84 O
HETATM 5239 O5 IPM A 800 -7.144 -37.476 15.058 1.00 31.69 O
HETATM 5240 MN MN A 999 -8.723 -38.606 18.552 1.00 32.82 MN
HETATM 5241 C1 IPM B 800 0.061 -60.470 18.277 1.00 34.25 C
HETATM 5242 C2 IPM B 800 1.493 -60.050 18.586 1.00 33.41 C
HETATM 5243 C3 IPM B 800 2.328 -59.974 17.293 1.00 31.13 C
HETATM 5244 C4 IPM B 800 1.610 -58.994 16.347 1.00 33.86 C
HETATM 5245 C5 IPM B 800 3.791 -59.540 17.568 1.00 30.97 C
HETATM 5246 C6 IPM B 800 4.631 -59.454 16.286 1.00 34.00 C
HETATM 5247 C7 IPM B 800 4.498 -60.449 18.600 1.00 35.10 C
HETATM 5248 O1 IPM B 800 1.462 -58.722 19.171 1.00 34.28 O
HETATM 5249 O2 IPM B 800 -0.132 -61.583 17.871 1.00 35.75 O
HETATM 5250 O3 IPM B 800 -0.898 -59.572 18.487 1.00 35.55 O
HETATM 5251 O4 IPM B 800 0.739 -59.499 15.489 1.00 34.59 O
HETATM 5252 O5 IPM B 800 1.881 -57.816 16.391 1.00 34.56 O
HETATM 5253 MN MN B 999 -0.582 -57.882 19.668 1.00 35.31 MN
HETATM 5254 MN MN B1000 0.167 -72.983 -0.484 0.50 40.96 MN
HETATM 5255 MN MN B1001 -20.889 -89.868 22.551 0.50 41.80 MN

[zcx@umich.edu]

If there are multiple instances of the same type of ligand in the same chain, they will be sequentially labeled as 1,2,3, ... by ligand serial number, For example, PDB 117e chain B has four copies of MN ligands, which have ligand serial number of 1, 2, 3, and 4, respectively.

I am afraid you made a mistake for the binding site number code for 2y41 chain B. It has three binding sites:
BS01 for IPM from chain A
BS02 for IPM from chain B
BS03 for MN from chain B
There is no IPM for BS03 of 2y41 chain B.