Representative Protein Database

Simon Brocklehurst simon.brocklehurst at
Mon Feb 5 06:58:18 EST 2001

Scott LeGrand wrote:

> Which leads to my question.  How big does a protein need to be before it can form a
> stable hydrophobic core (without any disulfides) that can exist long-term in
> solution?  I want to extract a database of such proteins both to generate
> energy function parameters and to use as targets for conformational search.  I
> would like to limit the size of my proteins so that conformational serach is
> manageable.
> Any ideas?

Hi Scott,

You might want to check out:

The high-resolution structure of the peripheral subunit-binding domain of
dihydrolipoamide acetyltransferase from the pyruvate dehydrogenase multienzyme complex
of Bacillus stearothermophilus.

Kalia YN, Brocklehurst SM, Hipps DS, Appella E, Sakaguchi K, Perham RN

J Mol Biol 1993 Mar 5;230(1):323-41

>From the abstract:

The structured region of the binding domain, comprising 33 residues, represents an
exceptionally short amino acid sequence with defined tertiary structure that has no
disulphide bond, ligand or cofactor to stabilize the fold. It may be approaching the
lower size limit for a three-dimensional structure possessing features characteristic
of larger structures, including a close-packed, non-polar interior. The organization of
the side-chains in the hydrophobic core may have implications for de novo protein

In terms of the coordinates, make sure you get them from PDB entry 2PDD (the ensemble),
and NOT 2PDE which is completely ******* (the PDB's fault not mine - I  tried several
times years ago (when it was still Brookhaven) to get them to fix their ****-up, but
they never bothered).

Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
mailto:simon.brocklehurst at

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