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This Search page includes the following Search Options:

• PDB/NDB code
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In addition, PDB/SWISS-PROT cross reference lists and the NCBI-based Genus/Species Classification can be browsed.

The PDB/SWISS-PROT cross reference compilations are listed by:

• PDB code
• SWISS-PROT entry name
• SWISS-PROT protein name
• SWISS-PROT species name.

The NCBI-based Genus/Species Classification offers:

• PDB Structures Genus Listing
  • Alphabetical Listing
  • Listing by Number of Structures Known for a Genus
  • Listing by Deposition Date of the Very First Structure of the Genus (Genus Timeline)
• PDB Structures Species Listing
  • Alphabetical Listing
  • Listing by Number of Structures Known for a Species
  • Listing by Deposition Date of the Very First Structure of a Species (Species Timeline)
• PDB Structures Species Statistics
  • Cumulative Species Number and Species Number per Year in the Protein Data Bank
  • Total Number of PDB Structures Analyzed:
  • Number of Structures with Species Information Assigned:
  • Number of Structures with no Species Information Assigned:
  • Number of Protein Structures with no Species Information Assigned:
  • Number of Genuses Occurring in PDB Structures:
  • Number of Species Occurring in PDB structures:

The PDB code consists of 4 characters the first of which is a digit in the range 0-9; the remaining 3 are alpha-numeric. Entries with a 0 as the first character do not contain coordinate data and are not accessible by this search option.

See the PDB Contents Guide for more detailed information on all aspects of information provided by the PDB (141 pages, 370 kBytes, PDF Format)

The NDB code consists of 6 or 7 characters. Even though the first two of them seem to indicate nucleic acid conformation and structure, there is no direct relationship between code and structure type intended.

Via the NDB classification of nucleic acid structures you can get an impression of the code.

For both the PDB and NDB codes partial string matching is not allowed.

The SWISS-PROT entry name has the general structure X_Y.

X is a mnemonic code of at most 4 alphanumeric characters representing the protein name. For example, INS represents insulin.

Y is a mnemonic code of at most 5 alphanumeric characters representing the biological source of the protein. This code is generally made of the first three letters of the genus and of the first two letters of the species. For example, _PSEPU stands for Pseudomonas putida. However, for the 16 most commonly occurring species in the database self-explanatory names are used, such as _HUMAN for Human and _ECOLI for Escherichia coli.

The purpose of the SWISS-PROT accession numbers is to provide a stable way of identifying entries from release to release. It is sometimes necessary to change the entry names. Accession numbers are never changed. Entries have more than one accession number if they have been merged or split. An example for a valid accession number is P04179.

More information can be obtained from the SWISS-PROT User Manual.

One can search either for the SWISS-PROT entry name or for any of the accession numbers.

Partial string matching with a minimumof three characters is allowed for the SWISS-PROT entry names and accession numbers.

A search for SODM_ returns all superoxide dismutase PDB structures and a search for _ECOLI all PDB protein entries from E. coli. Searching for SODM_ECOLI results in the five PDB entries (June 27, 2001): 1d5n, 1i08, 1i0h, 1mmm, 1vew. The same result is obtained when searching for the accession number P00448. On the atlas pages of any of these entries the other four ones are listed as related entries with the same SWISS-PROT code.

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