Primary Protein and Nucleic Acid Three‐dimensional Structure Databases


All the publicly accessible three‐dimensional structures of proteins, DNA, RNA and complexes thereof, which have been determined experimentally by X‐ray crystallography or nuclear magnetic resonance, are maintained in the Protein Data Bank (PDB).

Keywords: structure databases; Protein Data Bank; PDB; Nucleic Acid DataBase; NDB

Figure 1.

Atomic structure of the oxygen transport myoglobin (PDB identifier 1mbn) showing the oxygen bound to the haem. The protein is depicted as a ribbon that highlights the α‐helical secondary structure. The haem atoms are shown as spheres with the oxygen (red) surrounded by four nitrogen atoms (blue).

Figure 2.

Growth of the Protein Data Bank (PDB) shown as the number of structures deposited and released as a function of year. Last update 17 April 2000.

Figure 3.

Atomic structure of bacteriophage ϕX174 showing the icosohedral assembly of the capsid (PDB identifier 1cd3).

Figure 4.

Flow chart of the Protein Data Bank (PDB) query system showing the types of query and the results generated.


Further Reading

Berman HM, Olson WK, Beveridge DL et al. (1992) The Nucleic Acid Database: a comprehensive relational database of three‐dimensional structures of nucleic acids. Biophysical Journal 63: 751–759.

Berman HM, Westbrook J, Feng Z et al. (2000) The Protein Data Bank. Nucleic Acids Research 28: 235–242.

Branden C‐I and Tooze J (1999) Introduction to Protein Structure, 2nd edn. New York: Garland.

Murzin AG, Brenner SE, Hubbard T and Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247: 536–540.

Wang Y, Addess KJ, Geer L et al. (2000) MMDB: 3D structure data in Entrez. Nucleic Acids Research 28: 243–245.

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Bourne, Philip E(Feb 2002) Primary Protein and Nucleic Acid Three‐dimensional Structure Databases. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0003030]