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Protein Data Bank
Protein Data Bank
Contents
The PDB database is updated weekly (UTC+0 Wednesday), along with its
holdings list.[16] As of 10 January 2023, the PDB comprised:
Protein/Nucleic Nucleic
Experimental Proteins Proteins with Oligosaccharides
Acid Acids Other Total
Method only oligosaccharides only
complexes only
X-ray
152277 8969 8027 2566 163 11 172013
diffraction
NMR 12104 32 281 1433 31 6 13887
Electron
9226 1633 2898 77 8 0 13842
microscopy
Hybrid 189 7 6 12 0 1 215
Neutron 72 1 0 2 0 0 75
Other 32 0 0 1 0 4 309
Total: 173900 10642 11212 4091 202 22 200069
Most structures are determined by X-ray diffraction, but about 7% of structures are determined by protein NMR.
When using X-ray diffraction, approximations of the coordinates of the atoms of the protein are obtained, whereas
using NMR, the distance between pairs of atoms of the protein is estimated. The final conformation of the protein
is obtained from NMR by solving a distance geometry problem. After 2013, a growing number of proteins are
determined by cryo-electron microscopy.
For PDB structures determined by X-ray diffraction that have a structure factor file, their electron density map may
be viewed. The data of such structures may be viewed on the three PDB websites.
Historically, the number of structures in the PDB has grown at an approximately exponential rate, with 100
registered structures in 1982, 1,000 structures in 1993, 10,000 in 1999, 100,000 in 2014, and 200,000 in January
2023.[17][18]
File format
The file format initially used by the PDB was called the PDB file format. The original format was restricted by the
width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic
Information file" format, mmCIF, which is an extension of the CIF format was phased in. mmCIF became the
standard format for the PDB archive in 2014.[19] In 2019, the wwPDB announced that depositions for
crystallographic methods would only be accepted in mmCIF format.[20]
An XML version of PDB, called PDBML, was described in 2005.[21] The structure files can be downloaded in
any of these three formats, though an increasing number of structures do not fit the legacy PDB format. Individual
files are easily downloaded into graphics packages from Internet URLs:
The "4hhb" is the PDB identifier. Each structure published in PDB receives a four-character alphanumeric
identifier, its PDB ID. (This is not a unique identifier for biomolecules, because several structures for the same
molecule—in different environments or conformations—may be contained in PDB with different PDB IDs.)
See also
Crystallographic database
Protein structure
Protein structure prediction
Protein structure database
PDBREPORT lists all anomalies (also errors) in PDB structures
PDBsum—extracts data from other databases about PDB structures
Proteopedia—a collaborative 3D encyclopedia of proteins and other molecules
[1] (https://pdb101.rcsb.org/)
References
1. wwPDB, Consortium (2019). "Protein Data Bank: the single global archive for 3D macromolecular
structure data" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324056). Nucleic Acids Res. 47
(D1): 520–528. doi:10.1093/nar/gky949 (https://doi.org/10.1093%2Fnar%2Fgky949).
PMC 6324056 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324056). PMID 30357364 (https://
pubmed.ncbi.nlm.nih.gov/30357364).
2. "PDBe home < Node < EMBL-EBI" (http://www.pdbe.org/). pdbe.org.
3. "Protein Data Bank Japan – PDB Japan – PDBj" (https://www.pdbj.org/). pdbj.org.
4. Bank, RCSB Protein Data. "RCSB PDB: Homepage" (http://www.rcsb.org/). rcsb.org.
5. "Biological Magnetic Resonance Bank" (http://www.bmrb.wisc.edu). bmrb.wisc.edu.
6. Berman, H. M. (January 2008). "The Protein Data Bank: a historical perspective" (http://journals.iuc
r.org/a/issues/2008/01/00/sc5004/sc5004.pdf) (PDF). Acta Crystallographica Section A. A64 (1):
88–95. doi:10.1107/S0108767307035623 (https://doi.org/10.1107%2FS0108767307035623).
PMID 18156675 (https://pubmed.ncbi.nlm.nih.gov/18156675).
7. Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (December 1997).
"PDBsum: a Web-based database of summaries and analyses of all PDB structures". Trends
Biochem. Sci. 22 (12): 488–90. doi:10.1016/S0968-0004(97)01140-7 (https://doi.org/10.1016%2FS
0968-0004%2897%2901140-7). PMID 9433130 (https://pubmed.ncbi.nlm.nih.gov/9433130).
8. Meyer EF (1997). "The first years of the Protein Data Bank" (https://www.ncbi.nlm.nih.gov/pmc/artic
les/PMC2143743). Protein Science. Cambridge University Press. 6 (7): 1591–1597.
doi:10.1002/pro.5560060724 (https://doi.org/10.1002%2Fpro.5560060724). PMC 2143743 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC2143743). PMID 9232661 (https://pubmed.ncbi.nlm.nih.go
v/9232661).
9. "Protein Data Bank" (https://doi.org/10.1038%2Fnewbio233223b0). Nature New Biology. 233.
1971. doi:10.1038/newbio233223b0 (https://doi.org/10.1038%2Fnewbio233223b0).
10. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE
(January 2000). "The Protein Data Bank" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472).
Nucleic Acids Res. 28 (1): 235–242. doi:10.1093/nar/28.1.235 (https://doi.org/10.1093%2Fnar%2F
28.1.235). PMC 102472 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472). PMID 10592235
(https://pubmed.ncbi.nlm.nih.gov/10592235).
11. "Research Collaboratory for Structural Bioinformatics" (https://web.archive.org/web/200702050000
27/http://home.rcsb.org/). RCSB.org. Research Collaboratory for Structural Bioinformatics. Archived
from the original (http://home.rcsb.org/) on 2007-02-05.
12. "RCSB PDB Newsletter Archive" (http://www.rcsb.org/pdb/static.do?p=general_information/news_
publications/newsletters/newsletter.html). RCSB Protein Data Bank.
13. Curry E, Freitas A, O'Riáin S (2010). "The Role of Community-Driven Data Curation for
Enterprises" (https://books.google.com/books?id=DsMrnk9-4NsC&pg=PA25). In D. Wood (ed.).
Linking Enterprise Data. Boston: Springer US. pp. 25–47. ISBN 978-1-441-97664-2.
14. "PDB Validation Suite" (http://sw-tools.pdb.org/apps/VAL/index.html). sw-tools.pdb.org.
15. Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Costanzo LD, et al. (wwPDB consortium)
(January 2019). "Protein Data Bank: the single global archive for 3D macromolecular structure
data" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324056). Nucleic Acids Research. 47 (D1):
D520–D528. doi:10.1093/nar/gky949 (https://doi.org/10.1093%2Fnar%2Fgky949). PMC 6324056
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324056). PMID 30357364 (https://pubmed.ncbi.nl
m.nih.gov/30357364).
16. "PDB Current Holdings Breakdown" (https://web.archive.org/web/20070704045207/http://www.rcs
b.org/pdb/statistics/holdings.do). RCSB. Archived from the original (http://www.rcsb.org/pdb/statistic
s/holdings.do) on 2007-07-04. Retrieved 2007-07-02.
17. Anon (2014). "Hard data: It has been no small feat for the Protein Data Bank to stay relevant for
100,000 structures" (https://doi.org/10.1038%2F509260a). Nature. 509 (7500): 260.
doi:10.1038/509260a (https://doi.org/10.1038%2F509260a). PMID 24834514 (https://pubmed.ncbi.
nlm.nih.gov/24834514).
18. Protein Data Bank. "PDB Statistics: Overall Growth of Released Structures Per Year" (https://www.r
csb.org/stats/growth/growth-released-structures). www.rcsb.org. Retrieved 12 January 2023.
19. "wwPDB: File Formats and the PDB" (https://www.wwpdb.org/documentation/file-formats-and-the-
pdb). wwpdb.org. Retrieved April 1, 2020.
20. wwPDB.org. "wwPDB: 2019 News" (https://www.wwpdb.org/news/news?year=2019#5d17c1ceea
7d0653b99c87e2). wwpdb.org.
21. Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM (April 2005). "PDBML: the representation
of archival macromolecular structure data in XML" (https://doi.org/10.1093%2Fbioinformatics%2Fbt
i082). Bioinformatics. 21 (7): 988–992. doi:10.1093/bioinformatics/bti082 (https://doi.org/10.1093%2
Fbioinformatics%2Fbti082). PMID 15509603 (https://pubmed.ncbi.nlm.nih.gov/15509603).
22. "ICM-Browser" (http://www.molsoft.com/icm_browser.html). Molsoft L.L.C. Retrieved 2013-04-06.
23. "Swiss PDB Viewer" (http://www.expasy.ch/spdbv/mainpage.html). Swiss Institute of
Bioinformatics. Retrieved 2013-04-06.
24. "STAR: Biochem - Home" (http://web.mit.edu/star/biochem). web.mit.edu.
25. "VisProt3DS" (http://www.molsystems.com/vp3ds.html). Molecular Systems Ltd. Retrieved
2013-04-06.
External links
The Worldwide Protein Data Bank (wwPDB) (http://www.wwpdb.org/)—parent site to regional
hosts (below)
RCSB Protein Data Bank (http://www.rcsb.org) (USA)
PDBe (http://www.pdbe.org/) (Europe)
PDBj (https://www.pdbj.org/) (Japan)
BMRB, Biological Magnetic Resonance Data Bank (http://www.bmrb.wisc.edu/) (USA)
wwPDB Documentation (http://www.wwpdb.org/docs.html)—documentation on both the PDB and
PDBML file formats
Looking at Structures (http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Struct
ures/intro.html) Archived (https://web.archive.org/web/20110324191425/http://www.rcsb.org/pdb/sta
tic.do?p=education_discussion%2FLooking-at-Structures%2Fintro.html) 2011-03-24 at the
Wayback Machine—The RCSB's introduction to crystallography
PDBsum Home Page (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/)—Extracts data from
other databases about PDB structures.
Nucleic Acid Database, NDB (http://ndbserver.rutgers.edu/index.html)—a PDB mirror especially for
searching for nucleic acids
Introductory PDB tutorial sponsored by PDB (https://web.archive.org/web/20140202193642/http://w
ww.openhelix.com/pdb)
PDBe: Quick Tour on EBI Train OnLine (http://www.ebi.ac.uk/training/online/course/pdbe-quick-tou
r)