Downloading PDB Files
The following lists a sample of Internet sites from which you can download PDB files
For further PDB mirrors refer to the end of the PDB newsletter
- 1) The Protein Data Bank (PDB) at Brookhaven National Laboratories, U.S.
- The PDB can be accessed via the WWW at:
The URL for a PDB file is:
where **** is the 4-letter code.
The Brookhaven PDB anonymous ftp and gopher servers are at pdb.pdb.bnl.gov
ie. if accessed with a WWW browser the URLs are
/current_release/ contains directories
uncompressed_files/, each of which
contains directories named after the 2nd and 3rd letters of the PDB files they
contain- (as in EMBL site, see below);
the URL is currently of the form
The Brookhaven PDB WWW home page is at http://www.pdb.bnl.gov
- 2) PDB Browser at ExPASy
(Experimental Protein Analysis System, University of Geneva)
- The URL for a PDB file with code **** is
- 3) The anonymous ftp server of EMBL, Heidelberg, Germany
in directory /pub/databases/pdb/current/
Please read the text in this directory
(Access via WWW by clicking on
The subdirectory compressed/ contains many sub-directories, all of
which have 2-character names- they correspond to the 2nd and 3rd
characters of the code of the PDB files they contain, e.g. 1abc
would be stored in directory
The filenames are of the form pdb****.ent and can also be obtained
in Unix-compressed format.
The EMBL WWW home page is at http://www.embl-heidelberg.de/
- 4) The PDB Browser at the Martin Luther University, Halle-Wittenberg,
- The URL is of the form:
- 5) The PDB Browser at the Institute of Biochemistry and Biophysics,
Warsaw (The Polish National EMBnet Node)
- Use http://www.ibb.waw.pl/WWWBrowse/send-image?filename=****
where **** is the 4-character code.
- 6) Birkbeck College Crystallography Department also has a PDB mirror.
- A PDB file can be obtained from the URL
where **** is the 4-character code. Note that if you have your browser
configured for chemical-MIME, the structure will be fed straight into
Rasmol! Alternatively, proceed to the URL
where ** are the 2nd and 3rd characters of the 4-character code; you
will receive a menu of PDB files. You can retrieve any one of them
by using the "Save Link As" option of your WWW browser, e.g. with some
versions of Netscape and Mosaic, hold down the Shift key while clicking
on the link. With later versions of Netscape clicking on a link with
the right mouse button has the same effect.
The PPS Organizers
Last updated 7th May '96