Protein Data Bank (file format)

pdb

Filename extension	.pdb, .ent, .brk
Internet media type	chemical/x-pdb
Type of format	chemical file format

The Protein Data Bank (pdb) file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. Most of the information in that database pertains to proteins, and the pdb format accordingly provides for rich description and annotation of protein properties. However, proteins are often crystallized in association with other molecules or ions such as water, ions, nucleic acids, drug molecules and so on, which therefore can be described in the pdb format as well.

Example

A typical pdb file describing a protein consists of hundreds to thousands of lines like the following (taken from a file describing the structure of a synthetic collagen-like peptide :

HEADER    EXTRACELLULAR MATRIX                    22-JAN-98   1A3I
TITLE     X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE
TITLE    2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)
...
EXPDTA    X-RAY DIFFRACTION
AUTHOR    R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA,
AUTHOR   2 B.BRODSKY,A.ZAGARI,H.M.BERMAN
...
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
...
SEQRES   1 A    9  PRO PRO GLY PRO PRO GLY PRO PRO GLY
SEQRES   1 B    6  PRO PRO GLY PRO PRO GLY
SEQRES   1 C    6  PRO PRO GLY PRO PRO GLY
...
ATOM      1  N   PRO A   1       8.316  21.206  21.530  1.00 17.44           N
ATOM      2  CA  PRO A   1       7.608  20.729  20.336  1.00 17.44           C
ATOM      3  C   PRO A   1       8.487  20.707  19.092  1.00 17.44           C
ATOM      4  O   PRO A   1       9.466  21.457  19.005  1.00 17.44           O
ATOM      5  CB  PRO A   1       6.460  21.723  20.211  1.00 22.26           C
...
HETATM  130  C   ACY   401       3.682  22.541  11.236  1.00 21.19           C  
HETATM  131  O   ACY   401       2.807  23.097  10.553  1.00 21.19           O  
HETATM  132  OXT ACY   401       4.306  23.101  12.291  1.00 21.19           O          
...

ATOM records

describe the coordinates of the atoms that are part of the protein. For example, the first ATOM line above describes the alpha-N atom of the first residue of peptide chain A, which is a proline residue; the first three floating point numbers are its x, y and z coordinates and are in units of Ångströms. The next three columns are the occupancy, temperature factor, and the element name, respectively.

HETATM records

describe coordinates of hetero-atoms, that is those atoms which are not part of the protein molecule.

SEQRES records

give the sequences of the three peptide chains (named A, B and C), which are very short in this example but usually span multiple lines.

REMARK records

can contain free-form annotation, but they also accommodate standardized information; for example, the REMARK 350 BIOMT records describe how to compute the coordinates of the experimentally observed multimer from those of the explicitly specified ones of a single repeating unit.

HEADER, TITLE and AUTHOR records

provide information about the researchers who defined the structure; numerous other types of records are available to provide other types of information.

Through the years the file format has undergone many changes and revisions. Its original format was dictated by the width of computer punch cards (80 columns). The most recent revision is 3.2.

See also

• Chemical file format
• ScientificPython — provides an interface for Python
• The protein data bank

Molecular visualization software capable of displaying pdb files:

• Coot_(program)
• Jmol
• PyMOL
• RasMol
• VMD
• Gabedit
• Molden
• Molekel
• Software for molecular mechanics modeling
• Cn3D

External links

• PDB Format Guide This is the current version (3.2) of the PDB format specification.
• PDBML An more recent, alternative XML-based file format for molecular coordinates.
• The RCSB Protein Data Bank
• Protein Data Bank in Europe
• The Molecular Modeling DataBase (MMDB) from NCBI
• The Data Uniformity Project from PDB
• MakeMultimer An online tool for expanding BIOMT records in pdb files