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PDB/UniProt Mapping

Interrogate the mapping from your scripts

You may also access the mapping directly from your scripts using a URL of the form: http://www.bioinf.org.uk/cgi-bin/pdbsws/query.pl?plain=1&qtype=ttt&id=iii&chain=ccc&res=rrr

The fields in the URL are as follows:

FieldMeaning
plain=1This causes the CGI script to generate plain parsable text rather than HTML
all=yesThis causes a full alignment to be printed
qtype=tttttt is the query type which may be pdb, ac, or id
id=iiiiii is the PDB code, SwissProt identifier, or UniProt accession
chain=cccccc is the chain label used only when the query type is PDB
res=rrrrrr is the PDB residue identifier, or the residue number in the UniProt entry

For example:

Results

The results are returned in the form:

KeywordMeaning
PDB:PDB code
CHAIN:chain label
RESID:PDB residue id
PDBAA:Amino acid present in the PDB file
AC:UniProt accession
ID:UniProt identifier
UPCOUNT:Residue number in the UniProt sequence
UPAA:Amino acid present in the UniProt file
START:First residue in the PDB chain (if known)
STOP:Last residue in the PDB chain (if known)
ERROR:Error message (if any - database connectivity)

The RESID: PDBAA: UPCOUNT: and UPAA: fields will only be provided if a residue number has been used in the search.

Perl Modules

Two Perl modules are provided to make this easier from within your code