Missing parts of polysaccharide ligands?
Posted: Wed Jan 15, 2025 2:30 am
Hello,
I see there is a lot of spam here, I hope this comes through okay. I'm starting to work with BioLiP2, and investigating some of the data, I see that in some examples at least there are polysaccharides in the original PDB, but BioLiP identifies a binding site around just one of the sugar residues. For instance, compare https://www.rcsb.org/structure/1gwl to https://seq2fun.dcmb.med.umich.edu//Bio ... =A&bs=BS02. It appears that of a six-sugar chain, only one is present in BioLiP (there are two other sites listed for this structure, with similar results). Is this expected?
Thank you,
Marcus D. Collins, Ph.D.
I see there is a lot of spam here, I hope this comes through okay. I'm starting to work with BioLiP2, and investigating some of the data, I see that in some examples at least there are polysaccharides in the original PDB, but BioLiP identifies a binding site around just one of the sugar residues. For instance, compare https://www.rcsb.org/structure/1gwl to https://seq2fun.dcmb.med.umich.edu//Bio ... =A&bs=BS02. It appears that of a six-sugar chain, only one is present in BioLiP (there are two other sites listed for this structure, with similar results). Is this expected?
Thank you,
Marcus D. Collins, Ph.D.