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protein / PDB file structure

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protein / PDB file structure

Postby mmukhin » Tue Nov 17, 2009 12:23 am

Hello,
I've been working on a project trying to measure rates of enzymatic reactions.

I sometimes come accross PDB files that seem to have a very symmetrical shape. Are they just shaped this way, or was there a stereo/mirror/etc structure put alongside the original?

http://www.pdb.org/pdb/explore.do?structureId=1DC4

I cant really find any others right now.
Also, for RuBisCo: http://www.pdb.org/pdb/explore.do?structureId=1RXO
Is that teh actual structure? It seems almost too-symmetrical.

Thank you!
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Re: protein / PDB file structure

Postby zami'87. » Tue Nov 17, 2009 3:29 am

Protein complex may look symmetrical if it's composed of many same/similar subunits...according to numbers of those subunits it can be for example tetramer 4(haemoglobin)..hexamer(6) (connexons, or proteasome-like complex in E. coli HslV)..heptamer,octamer...etc.
Nuclear pore complex has some symmetry...
Also many DNA binding proteins are dimers that bind to inverted repeats.
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Postby MrMistery » Wed Nov 18, 2009 4:14 am

rubisco has something like 16 subunits, 8 identical big subunits and 8 identical small subunits. So yeah, i think it's very symmetrical.
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