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, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which has kept data on biological macromolecules in the newer PDBx/mmCIF file format since 2014.[1]
| Filename extension |
.pdb, .ent, .brk |
|---|---|
| Internet media type |
chemical/x-pdb |
| Developed by | Protein Data Bank |
| Type of format | chemical file format |
| Container for | Molecule 3D structure, Protein tertiary structure |
| Extended to | mmCIF |
History
editThe PDB file format was invented in 1972[2][3] as a human-readable file that would allow researchers to exchange the atomic coordinates in a given protein through a database system. Its fixed-column width format is limited to 80 or 140[4] columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates.[5] Through the years the file format has undergone many changes and revisions. The final update to the PDB file format was in November 2012 with version 3.30.[6]
Example
editA 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.[7] 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
edit- SAMSON
- Athena
- BALLView
- Bioblender
- CCP4MG
- (UCSF) Chimera
- Cn3D
- Coot
- CueMol
- QuteMol
- Gabedit
- Materials and Processes Simulations (MAPS) platform
- Jmol
- Molden
- Molekel
- Open Visualization Tool(OVITO)
- PyMOL
- RasMol
- UGENE
- VisIt
- VMD
- WHAT IF
- Yasara
- Zeus molecular visualisation
- ePMV
- Discovery Studio
- ParaView
- UnityMol
3d Animation software capable of displaying PDB files
editSee also
edit- Chemical file format
- ScientificPython — provides an interface for Python
- Software for molecular mechanics modeling
References
edit- ^ Berman, Helen M.; Kleywegt, Gerard J.; Nakamura, Haruki; Markley, John L. (2014-10-01). "The Protein Data Bank archive as an open data resource". Journal of Computer-Aided Molecular Design. 28 (10): 1009–1014. doi:10.1007/s10822-014-9770-y. ISSN 1573-4951. PMC 4196035. PMID 25062767.
- ^ "wwPDB: File Format". www.wwpdb.org.
- ^ "PROTEIN DATABASE FILE RECORD FORMATS" (PDF). Retrieved 9 June 2024.
- ^ "PROTEIN DATABASE FILE RECORD FORMATS" (PDF). Retrieved 9 June 2024.
- ^ Berman, Helen M (2008). "The Protein Data Bank: a historical perspective". Acta Crystallographica. 64 (Pt 1): 88–95. doi:10.1107/S0108767307035623. ISSN 2053-2733. PMID 18156675.
- ^ "wwPDB: File Formats and the PDB". Protein Data Bank. Retrieved 2024-01-15.
- ^ "wwPDB Format version 3.3: Coordinate Section". Archived from the original on 2012-02-28. Retrieved 2012-03-23.
External links
edit- 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