Residue-level cross reference data based on PDB is available via SIFTS annotations.

Please check the following files at SIFTS Quick Access:

pdb_chain_uniprot.lst - A summary of the PDBe to UniProt residue level mapping, showing the start and end residues of the mapping using SEQRES, PDB sequence and UniProt numbering.

pdb_chain_pfam.lst - A summary of the Pfam domain identifier(s)(derived via the UniProt mapping) for each PDB chain that has been processed.

You can use two files and use one identifier to map to others. This is the best cross-reference for PDB-Uniprot-Pfam I could find. I am using this in my analysis.

Another answer for fun, using bio2rdf :-)

from http://uniprot.bio2rdf.org/sparql use the following query

select ?id ?pdb ?pfam  where {
?s <http://purl.org/dc/elements/1.1/identifier> ?id .
?s a <http://bio2rdf.org/core:Protein> .
?s  <http://www.w3.org/2000/01/rdf-schema#seeAlso>  ?pdb .  
?s  <http://www.w3.org/2000/01/rdf-schema#seeAlso>  ?pfam . 
FILTER regex(?pdb, "pdb:") 
FILTER regex(?pfam, "pfam:")

} limit 100 ##remove this for a larger answer

id  pdb     pfam
uniprot:P13744  http://bio2rdf.org/pdb:2E9Q     http://bio2rdf.org/pfam:PF00190
uniprot:P13744  http://bio2rdf.org/pdb:2EVX     http://bio2rdf.org/pfam:PF00190
uniprot:Q8GBW6  http://bio2rdf.org/pdb:1ON3     http://bio2rdf.org/pfam:PF01039
uniprot:Q8GBW6  http://bio2rdf.org/pdb:1ON9     http://bio2rdf.org/pfam:PF01039
uniprot:Q10666  http://bio2rdf.org/pdb:3C2G     http://bio2rdf.org/pfam:PF00505
uniprot:Q9FK25  http://bio2rdf.org/pdb:1NII     http://bio2rdf.org/pfam:PF08100
uniprot:Q9FK25  http://bio2rdf.org/pdb:1NII     http://bio2rdf.org/pfam:PF00891
uniprot:P31946  http://bio2rdf.org/pdb:2BQ0     http://bio2rdf.org/pfam:PF00244
uniprot:P31946  http://bio2rdf.org/pdb:2C23     http://bio2rdf.org/pfam:PF00244
uniprot:Q12802  http://bio2rdf.org/pdb:2DRN     http://bio2rdf.org/pfam:PF00169
(...)

It's all there on UniProt in "Cross-references", e.g. see this entry for NMB1681. The data is also available in the export formats, e.g. text format.

You might want to have a look at our BridgeDB, which was developed to help you solve questions like this. See: http://www.bridgedb.org

The file ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz seems to contain all the IDs.

curl  -s "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" |\
gunzip -c |\
egrep -i '(accession|pfam|pdb)'

  (...)
  <accession>P0C9E9</accession>
  <accession>P0C9K3</accession>
  <dbReference id="PF01639" key="10" type="Pfam">
  <accession>P0C9I4</accession>
  <dbReference id="PF01639" key="10" type="Pfam">
  (...)
  <property type="PDB accession" value="1KMH"/>
  (...)

There is also modern solution using data crossing softwares (ie : http://www.isoft.fr/bio/biopack_data_en.htm ). It definitly fills me with despair to see people "reinvent the wheel" for the main but only first step of their work : data access and mining ...

Using uniprot.org Using customize display in the uniprot entry view

Or using a mapping service http://www.uniprot.org/uniprot/?tab=mapping.

If you want to discuss the way uniprot maps to PDBe (not so straight forward as you might think) contact help@uniprot.org. Pfam comes directly out of the interpro results and there should not be that much skew between these databases.

You could try using the SRS service in the EBI.

http://srs.ebi.ac.uk/

This service links many databases with each other.

There is a tutorial available: http://www.embl.de/~seqanal/courses/srscourse/srstut.html

An example taken directly from this tutorial, the query: enzyme < pdb gives all the enzyme database entries for which the 3D structure is known!

I am planning to use a hash/checksum of the protein sequences to cross-link Uniprot to others.

SEquence Globally Unique IDentifier (SEGUID) is a hashing standard (based on SHA1) - it was specifically developed for uniquely identifying protein sequences.

See also: our PostgreSQL sequence-to-seguid implementation http://dba.stackexchange.com/questions/66/biological-sequences-of-uniprot-in-postgresql

This is a very old thread, however I still have not found a good way for pdb to uniprot residue mapping that doesn't rely on a web server that may not be up to date. SIFTS may be the way to go, but has a complicated data structure. Below is a simple self-contained biopython function which relies on an on-the-fly sequence alignment to determine the residue mapping. There may be more elegant ways to script this, but the following works.

from Bio.PDB import *
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.PDBList import PDBList
from Bio import pairwise2
from Bio import SeqIO

def resmap(chain, uniprot_sequence):
# Returns a PDB to UniProt residue number dictionary. 

    ppb=PPBuilder()
    polypeptides = ppb.build_peptides(chain)
    pdb_sequence = ""
    for polypeptide in polypeptides:
        pdb_sequence = pdb_sequence + polypeptide.get_sequence()
    pdb_res_nums = sortedres.id[1] for res in chain if res.id[0] == " ")

    residue_list = Selection.unfold_entities(chain, 'R')
    alignments = pairwise2.align.globalms(uniprot_sequence, pdb_sequence, 2, -1, -.5, -.1)    
    uniprot_align = str(alignments[0][0])
    pdb_align     = str(alignments[0][1])

    uniprot_map = []
    count = 0
    for residue in uniprot_align:
        if residue != "-":
            count += 1
            uniprot_map.append(count)
        else:
            uniprot_map.append(-1)

    pdb_map = []
    count = -1
    for residue in pdb_align:
        if residue != "-":
            count += 1
            pdb_map.append(pdb_res_nums[count])
        else:
            pdb_map.append(-1)

    matches = []
    for index, residue in enumerate(uniprot_map):
        if uniprot_align[index] == pdb_align[index] and uniprot_align[index] != "-" and pdb_align[index] != "-":
            matches.append(True)
        else:
            matches.append(False)

    mapping = {}
    for index, match in enumerate(matches):
        if match:
            mapping[pdb_map[index]] = uniprot_map[index]

    return mapping