Dear Thomas
There are several Ig-like domains that do not contain S-S bridges .
I am not aware of a software tool that does what you'd like. However, two key papers on the Ig-like fold (old but still very relevant) that might be useful to you are:
(1) Bork, Holm & Sander - The Immunoglobulin Fold. Strcutural Classification, Sequence Patterns and Common Core - J.Mol.Biol (1994) 242, 309-320.
(2) Harpaz & Chothia - Many of the Immunoglobulin Superfamily Domains in Cell Adhesion Molecules and Surface Receptors Belong to a New Structural Set Which is Close to That Containing Variable Domains - J. Mol. Biol. (1994), 238, 528-539.
With best wishes
Roberto
On 9 Oct 2014, at 08:42, Thomas Krey <[log in to unmask]> wrote:
> Dear all,
>
> I was wondering, if there is a tool out there that allows the easy classification of immunoglobulin and Ig-like domain subclasses based on a given pdb file. As far as I am aware the state-of-the-art for immunoglobulin domains is to determine the distance (in amino acids) between the two cysteines forming the canonical disulfide bond between strands B and F. However, I am facing a couple of Ig-like domains that do not contain this disulfide bond !
> Any help will be highly appreciated.
>
> Best regards
> Thomas
>
> Dr. Thomas Krey
> Institut Pasteur
> Structural Virology Unit
> 25-28 Rue du Docteur Roux
> 75015 Paris
> France
> [log in to unmask]
Roberto A. Steiner, PhD
Randall Division of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
[log in to unmask]
Phone 0044 20 78488216
Fax 0044 20 78486435
Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London
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