With respect to the following paper:

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

I have a few questions:

  1. in page 2, in the table, what does 501 mean in GLC-501(I searched for GLC-501 in PDB,couldnt find anything)

  2. in page 3, in the table, the cavity center column has got two entries, what does that mean? does one entry belong to the protein and another entry to the ligand(left for protein and right for ligand)??


1 Answer 1

  1. 501 denotes 501st residue in the corresponding PDB entry — 1BDG. See here

  2. A single protein can have multiple cavities (see here) and the multiple entries denote centres of different cavities.

  • $\begingroup$ so why exactly two has been given? Has this paper calculated these centers or are these available somewhere? $\endgroup$
    – girl101
    Commented May 18, 2015 at 4:45
  • $\begingroup$ and why is a number given to a residue? What does that imply? $\endgroup$
    – girl101
    Commented May 18, 2015 at 4:50
  • $\begingroup$ @user3237995 I am not an expert in this but I think all ligand residues are numbered in the PDB file. Just a way of listing the number of entities I guess. From this page: The ligand is assigned a unique residue number within chain to which it is bound. The residue that binds the ligand retains its standard name in both coordinate and SEQRES records. $\endgroup$
    Commented May 18, 2015 at 5:06
  • $\begingroup$ and why only two numbers listed? $\endgroup$
    – girl101
    Commented May 18, 2015 at 5:14
  • $\begingroup$ @user3237995 Regarding your first comment. Perhaps they are interested in checking all possible binding sites in the protein. And why 2 sites; perhaps there were not more. Note that some have three as well $\endgroup$
    Commented May 18, 2015 at 5:15

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