How can we classify our protein as an α, a β, an α/ β or an α + β protein?
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2.3 years ago
anasjamshed ▴ 120

I have visited PDB (https://www.rcsb.org) and entered the PDB code 1TTA into the search line. Then I used the 3D view tab in order to draw a topology diagram of either one of the subunits. How would I classify this protein as an α, a β, an α/β or an α + β protein?

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Is there a way to get the topology diagram of a protein at PDB from the viewer that shows the 3D structural model by default?
For that purpose I usually use PDBsum which has a 'Protein' tab for each PDB entry that includes protein:

The page under that tab also shows the wiring diagram illustrating the topology on the left side.

1ttadom-A01


The architecture classification is included under the 'Protein' tab as well, which comes from the same source as the information that Mensur Dlakic (@Mensur ) directed you to at the PDB.

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2.3 years ago
Mensur Dlakic ★ 27k

I am not sure if there is an automatic classification tool for this purpose. It is usually done by human experts, which is to say that you can't do it - I am assuming you are not an expert or else you wouldn't be asking.

Still, if you go to RCSB's page for 1TTA and click on the "Annotations" button, it will show you that this protein is All beta according to SCOP, beta sandwiches according to ECOD, and Mainly Beta according to CATH.

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I am not seeing any annotation button

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