PDB identification code: Difference between revisions
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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, without reference to the name of the molecule. | 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, without reference to the name of the molecule. | ||
There are over 400,000 possible 4-character PDB identification codes (419,904 or 466,560 if "0" is allowed as the first character). Thus, the | There are over 400,000 possible 4-character PDB identification codes (419,904 or 466,560 if "0" is allowed as the first character). Thus, the 63,500 entries in early 2010 have used up less than 14% 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== | ==See Also== | ||
*[http://pdbwiki.org/index.php/PDB_code PDB code at pdbwiki.org] | *[http://pdbwiki.org/index.php/PDB_code PDB code at pdbwiki.org] | ||
Revision as of 11:02, 19 February 2010
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, while the last three characters can be either numerals or letters. In the past, the first character was always a numeral in the range 1-9. Although there appear to be no entries beginning with "0", its exclusion may have been relaxed.
Every released entry in the PDB has an automatically-generated page in Proteopedia. Proteopedia is updated once each week, shortly following the weekly new release cycle at the PDB.
Examples:
- 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.
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, without reference to the name of the molecule.
There are over 400,000 possible 4-character PDB identification codes (419,904 or 466,560 if "0" is allowed as the first character). Thus, the 63,500 entries in early 2010 have used up less than 14% 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.