PDB identification code

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Every molecular model (atomic coordinate file) in the Protein Data Bank (PDB) has a unique accession or identification code. These codes are always 4 characters in length. The first character is a numeral in the range 1-9, while the last three characters can be either numerals (in the range 0-9) or letters.

Contents

Lower vs. Upper Case

PDB codes are often written in upper case. However, to avoid confusing zero (0) with the letter "O", lower case is helpful, for example 1o1o is clearer than 1O1O, and 2ou0 is clearer than 2OU0. (Also links to upper case codes in Proteopedia don't work! For example, 1O1O.) Depending on the font, number 1 can also be confused with capital "I" or lower case "L". So 1imo is clearer than 1IMO, but 1X9L is clearer than 1x9l.

PDB codes in Proteopedia

Every released entry in the PDB has an automatically-generated page in Proteopedia. To find it, simply enter the PDB code in the search slot found at the left of this (and every) page in Proteopedia. Proteopedia is updated once each week, shortly following the weekly new release cycle at the PDB. To link to a PDB code-titled page in Proteopedia, in the wikitext box, use double square brackets around the code. So for example, typing [[1vot]] when editing a Proteopedia article generates the link 1vot.

Examples of PDB Codes

  • 1mbn - a 1973 model of myoglobin, the first protein structure solved.
  • 1tna - a 1975 model of yeast phenylalanine transfer RNA, the first RNA structure solved.
  • 1bna - the first full turn of a B-form DNA double helix solved by crystallography. Solved in 1980, this confirmed, 27 years later, the 1953 theoretical model of Watson & Crick. In the intervening years, methods were developed for macromolecular crystallography, and for producing short segments of DNA of defined sequences. More...
  • 2hhd - human hemoglobin, deoxy.
  • 9ins - insulin.

Newer PDB Codes are Sequential

For many years, depositors of models could request an available PDB code that represented an acronym for the molecule represented. All the above examples are such cases. With the increase in number of new entries each week, the PDB no longer permits this option. In recent years, all PDB codes are assigned by the PDB from the pool of available codes, in sequential ascending order, without reference to the name of the molecule.

PDB codes are permanently associated with a single structure

Once a PDB code is assigned to a given structure, it's forever, even in those cases when a structure is withdrawn (retired from the database), like 3luw, or superceded by a newer or corrected structure, like 1ace. If requesting a page for a superseded structure, like 1aak, Proteopedia will automatically display the newest structure 2aak. Look for the explanation in the 'About this Structure' section of each page.

Limited Number of PDB Codes

There are over 419,904 possible 4-character PDB identification codes. This could be increased to 466,560 if "0" is allowed as the first character, but so far there are no plans to do this[1], Thus, the ~90,000 entries in early 2013 have used up ~21% of the available codes. Someday a scheme that can accomodate more entries will be required, requiring revision of macromolecular visualization and modeling software programs that obtain data online, all of which, of necessity, currently require 4-character PDB codes.

See Also

References

  1. In April, 2013. according to Rachel Kramer Green of the RCSB in Rutgers, NJ, there are no plans to use PDB codes beginning with 0.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky, Wayne Decatur

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