Citing PDB Structures

PDB entries are assigned a PDB ID that corresponds to a Digital Object Identifier (DOI) and in many cases, are described in a publication by the structure authors.

DOIs for PDB structures follow the format: 10.2210/pdbXXXX/pdb, where XXXX is replaced with the PDB ID (e.g.,10.2210/pdb4hhb/pdb). DOI citations should include the entry authors, deposition year, structure title, and DOI.

A PDB structure with a corresponding publication should be referenced by PDB ID and cited using both the corresponding DOI and publication.

For example:

PDB ID: 1ema

DOI Citation:
Ormo, M., Remington, S.J. (1996) Green fluorescent protein from Aequorea victoria doi: 10.2210/pdb1ema/pdb

Literature Citation:
Ormo, M., Cubitt, A.B., Kallio, K., Gross, L.A., Tsien, R.Y., Remington, S.J. (1996) Crystal structure of the Aequorea victoria green fluorescent protein Science 273: 1392-1395 doi: 10.1126/science.273.5280.1392

A PDB structure without a corresponding publication should be referenced by PDB ID and cited using the DOI Citation (entry authors, deposition year, structure title, and DOI):

PDB ID: 1ci0
DOI Citation:
Shi, W., Ostrov, D.A., Gerchman, S.E., Graziano, V., Kycia, H., Studier, B., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC) (1999) PNP Oxidase from Saccharomyces cerevisiae doi: 10.2210/pdb1ci0/pdb

Citing the wwPDB and the PDB archive

Reference wwPDB with the URL and the following citation:

H.M. Berman, K. Henrick, H. Nakamura (2003) Announcing the worldwide Protein Data Bank Nature Structural Biology 10 (12): 980

H.M. Berman, K. Henrick, H.Nakamura, J.L. Markley (2007) The Worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data Nucleic Acids Res. 35 (Database issue): D301-3

wwPDB consortium. (2019) Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res 47: D520-D528 doi: 10.1093/nar/gky949