File format for lig_pairs.lst file

This file lists the ligands in each PDB entry. A ligand is defined as a metal, small molecule, or peptide (of 10 residues or less) bound to a protein or DNA/RNA molecule.

Each line shows the PDB code, a colon and then a list of ligands found in that PDB entry, separated by semi-colons.

Ligand names are given as a sequence of 3-character "residue" names, separated by hyphens. Leading spaces in any residue name have been replaced by underscores, "_" (except where the ligand is a metal ion).

Where a ligand residue is a standard amino acid with an "attachment" (ie a modification consisting of an extra atom or atoms), the attachment is shown bracketed with a plus sign (see the "(+CH3)" and "(+SCC)" attachments in the examples below).

Example

1epn :  MOR-PHE-CYS(+CH3)-NOR; SO4;
1epo :  MOR-PHE-NLE-CHF-NME;   F;
1epp :  SO4; MAS-PHE-LYS-STA-DCI-MTF;
1epq :  PHE-GLY(+SCC)-XAO; SO4; SOT;
1epr :  DPH-HIS-CHF-EMR; TSM;   F;
1ept :   CA;
1epu :   SE;
1epv :  DCS;
1epw :  SO4;  ZN;
1epy :  SO4;  CL;  CO;
1epz :  TYD;
1eq2 :  NAP; ADQ;
1eq4 :   NA;
1eq5 :   NA;
1eq8 :  _OH;
1eq9 :  PMS;