[Dock-fans] Sequence and Structure Length doesn't Match

Scott Brozell sbrozell at rci.rutgers.edu
Wed Sep 8 10:01:46 PDT 2010


On Tue, Sep 07, 2010 at 09:44:21AM +0800, Mohd Afiq Hazlami wrote:
> Hi, I have a question. I got a crystallized protein structure from PDB
> that's 170 AA in length. But the complete sequence length of the protein I
> got from UniProt shows that the length is 529 AA. Is it okay to go through
> with the docking procedures with this protein? Thanks.

I've never used UniProt, but there are a lot of possible sources for
the length discrepancy.  You should scrutinize the pdb entry,
visualize it, read the refs, etc.
Some obvious possibilities are alternate or unresolved residues,
domains, etc.  Depending on the purpose of the docking these could be
fatal problems...

good luck,

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