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I am looking for PDB file for Osteopontin (SPP1). The entry- 3CXD shows the structure of an Osteopontin antibody, not of the protein itself. Thanks

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  • $\begingroup$ Is the structure known? $\endgroup$
    – terdon
    Apr 28, 2014 at 12:41
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    $\begingroup$ Apparently osteopontin lacks secondary structures. Only a 4-residue beta strand is reported in Uniprot. $\endgroup$
    – WYSIWYG
    Apr 28, 2014 at 14:03

2 Answers 2

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There doesn't seem to be a 3D structure of Osteopontin available, and after looking a bit at the literature about this protein I'm not really surprised.

Osteopontin is hypothesized to assume an elongated and flexible structure (Sodek et al., 2000). Flexible proteins are very hard to impossible to crystallize, typically the flexible parts are either removed or stabilized in some way. I'm not a crystallographer, but this protein doesn't look like it can be crystallized in the full form.

For NMR it is a bit on the large side, a full structure would likely be not feasible.

It also has extensive posttranslational modifications, which makes it much harder to produce in large amounts as needed for crystallography, and extremely expensive for NMR where you would have to isotope-label the protein as well.

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  • $\begingroup$ Thank Mad Scientist, I wanted to docking OPN with a small molecule. It seems it is impossible. $\endgroup$
    – Mahdi
    Apr 28, 2014 at 13:30
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only a small peptide of Osteopontin is available currently

http://www.rcsb.org/pdb/protein/P10451

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