Splitting PDB File into Chains and Ligands Without using Tools

SPLIT PDB File

Protein Data Bank (PDB) file format is a representation of a three-dimensional (3D) structure of the protein and ligand data extracted by interpreting the experimental result of high-energy electromagnetic radiation (X-ray) or Nuclear Magnetic Resonance (NMR) through the computational method. The standard PDB file format was created by RCSB during the 1970s for parsing through software.

The atomic coordinate entries of protein are represented by ATOM & TER fields, and ligand by HETATM field (given in the table below).

Record TypeColumnsDescription
ATOM1 - 4"ATOM"
7 - 11Atom serial number
13 - 16Atom name
17Alternate location indicator
18 - 20Residue name
22Chain identifier
23 - 26Residue sequence number
27Code for insertions of residues
31 - 38X orthogonal Å coordinate
39 - 46Y orthogonal Å coordinate
47 - 54Z orthogonal Å coordinate
55 - 60Occupancy
61 - 66Temperature factor
73 - 76Segment identifier
77 - 78Element symbol
79 - 80Charge
HETATM1 - 6"HETATM"
7 - 80same as ATOM records
TER1 - 3"TER"
7 - 11Serial number
18 - 20Residue name
22Chain identifier
23 - 26Residue sequence number
27Code for insertions of residues

Separation of PDB files to chains and ligands are most important in comparative/homology/molecular modelling and Computer-aided Drug Design. In this tutorial, a text editor is used to separate the PDB file into chains and ligands. The resource and software used in this video tutorial are RCSB PDB and Notepad++.

Note: The text editor must be an ASCII character only supported editor (not rich text editor). Moreover, the file name extension should end with .pdb.

Comments

Most Popular Posts

Technical Questions

RNA to Protein Translation in PERL

Simple Server and Client Chat using Python