Protein Data Bank (file format)
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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. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed sidechain rotamers, secondary structure assignments, as well as atomic connectivity. Structures are often deposited with other molecules such as water, ions, nucleic acids, ligands and so on, which can be described in the pdb format as well. The Protein Data Bank also keeps data on biological macromolecules in the newer mmCIF file format.
The PDB file format was invented in 1976 as a human-readable file that would allow researchers to exchange protein coordinates through a database system. Its original format was limited to 80 columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates. Through the years the file format has undergone many changes and revisions. As of 13 July 2011[update], the most recent revision is 3.30.
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 ...
- 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.
- REMARK records
- can contain free-form annotation, but they also accommodate standardized information; for example, the
REMARK 350 BIOMTrecords describe how to compute the coordinates of the experimentally observed multimer from those of the explicitly specified ones of a single repeating unit.
- 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.
- 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.
Molecular visualization software capable of displaying PDB files
- (UCSF) Chimera
- WHAT IF
- Zeus molecular visualisation
- Chemical file format
- ScientificPython — provides an interface for Python
- Software for molecular mechanics modeling
- PDB Format Guide This is the current version (3.3) of the PDB format specification.
- PDBML A 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 wwPDB remediation Project from wwPDB
- MakeMultimer An online tool for expanding BIOMT records in pdb files
- Molecules iPad/iPhone App to display PDB files
- Python Macromolecular Library (mmLib) — a Python library capable of reading and writing PDB file formats