puzzle picture
1984: TNK1 with Density
Status: Closed


Name: 1984: TNK1 with Density
Status: Closed
Created: 04/21/2021
Points: 100
Expired: 04/29/2021 - 18:00
Difficulty: Advanced
Description: Fold this TNK1 protein into the electron density map! TNK1 is a non-receptor protein tyrosine kinase NRPTK that has been implicated in the regulation of cell growth and cell death. This puzzle might be difficult, as this structure is not similar to known solved proteins. This electron density map comes from x-ray crystallography experiments, and outlines the shape of the folded protein. Help us determine the structure of this TNK1 variant by folding it in the electron density!
Categories: Electron Density, Overall, Prediction

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LociOiling's picture
User offline. Last seen 5 hours 21 min ago. Offline
Joined: 12/27/2012
hiding out...

This advanced puzzle appears after the design of the month and protein design sandbox puzzles in the puzzle menu. You have to scroll the puzzle list to find it.

Joined: 06/06/2013
Groups: Gargleblasters
is there a print protein?

I can't see anything in ED cloud. I usually fold and then insert into the cloud and adjust. Is there a list of the AAs?

Joined: 03/30/2013
Groups: Go Science

1234567890 1234567890 1234567890 1234567890 1234567890 1234567890


Joined: 03/30/2013
Groups: Go Science
First 70 residues

The first 70 residues seem to be the 2TEL crystallization module. see PDB 2QB1 amongst others. This factoid might be useful for getting started.

Joined: 06/06/2013
Groups: Gargleblasters
thanks JM


Susume's picture
User offline. Last seen 8 hours 41 min ago. Offline
Joined: 10/02/2011
Nice density

I have to say this is a nice density - you can see many of the carbonyls clearly (the little red-tipped twigs all along the backbone that you can see in 'Stick' view with 'Ligand Specific' or some of the other color schemes). In a helix, the twigs will all point toward the higher-numbered end of the helix, and will H-bond to the blue elbows that are also part of the backbone. Some of these H-bonds can be seen in the density cloud too. Turn on 'Show bonds- Helix' in View menu to see them.

LociOiling's picture
User offline. Last seen 5 hours 21 min ago. Offline
Joined: 12/27/2012

See stick view and helices" for an example of the twigs and elbows. I'm still working on a good example showing the hydrogen bonds in the density....

LociOiling's picture
User offline. Last seen 5 hours 21 min ago. Offline
Joined: 12/27/2012

Just for the record, AA Edit 2.0.1 gets you the primary structure in easy to use string format.

JPred is one place you can use that primary structure string. JPred finds any PDB matches, and it can also do a secondary structure prediction.

Searching for a primary structure directly in the PDB at rcsb.org is more difficult. Just pasting the string into the search box hasn't worked for some time. Instead, you have to drill down to the Sequence section of the Advanced Search Query Builder and enter the string there. Then select "Polymer Entities" under "Display Results As". The rscb.org results are more graphically oriented that JPred's simple text output.

print protein 2.9.2 is the recipe that gives you primary structure, secondary structure, and so much more.

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