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Structure database: PDB. Tuomas Hätinen. Protein Data Bank. A repository for 3-D biological macromolecular structure. It includes proteins, nucleic acids and viruses. Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%). Protein Data Bank.

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Structure database pdb l.jpg

Structure database: PDB

Tuomas Hätinen


Protein data bank l.jpg
Protein Data Bank

  • A repository for 3-D biological macromolecular structure.

  • It includes proteins, nucleic acids and viruses.

  • Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%).


Protein data bank3 l.jpg
Protein Data Bank

  • Founded in 1971 by Brookhaven National Laboratory, New York.

  • Transferred to the Research Collaboratory for Structural Bioinformatics (RCSB) in 1998.

  • Currently it holds 40,000 released structures.



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PDB data formats

  • PDB file format was used to contain the coordinates and related information.

  • In the late 1990’s, macromolecular Crystallographic Information file (mmCIF) evolved.

  • mmCIF and PDBML

    • Push in to make structure files completely self-contained descriptions of the experiment and details of the structure determination.

    • PDB file format unstructured and obsolete


Pdb file format l.jpg
PDB File Format

  • Text file – you can edit with a text editor e.g. WordPad

  • Atomic co-ordinates

  • Rich annotation

    • Citation

    • Experimental Method

    • Biological source e.

    • Etc.