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Why do I find many cross-references to PDB in UniProtKB/Swiss-Prot?

Last modified September 3, 2013

Some proteins are highly popular because they are of medical interest or can be used in biotechnology. As an example, human Thrombin (P00734) has a very important role in blood clotting, and mutations in this protein can cause dysprothrombinemia, a rare inherited blood clotting disorder.

As a consequence, there is more than one cross-reference to PDB because a number of different structures are available for this protein. Thrombin structures differ for a number of reasons: 1) their resolutions are not the same, 2) some structures apply to the apoprotein while some others apply to the Thrombin complexed with various ligands. The following structures are Thrombin complexed with 4 different inhibitors: 1A2C,1A3B,1A3E,1A46. What is more, scientists have also studied the 3D structures of various mutants.

3D structures convey important experimental evidence on a protein: its secondary structure, how it is folded, which parts of the polypeptide chain are available for interactions with other proteins, which residues are directly involved in the catalytic activity, in metal-binding, etc.

Because 3D structures are so important, we endeavour to be as up-to-date as possible and to show all available cross-references to PDB from proteins in our knowledgebase.