LociOiling Lv 1
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1984: TNK1 with Density
Closed since almost 5 years ago
Advanced Overall Prediction Electron DensitySummary
- Created
- April 21, 2021
- Expires
- Max points
- 100
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!
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Comments
Skippysk8s Lv 1
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?
Anfinsen_slept_here Lv 1
1234567890 1234567890 1234567890 1234567890 1234567890 1234567890
PAHLRLQPIY WSRDDVAQWL KWAENEFSLS PIDSNTFEMN GKALLLLTKE DFRYRSPHSG DELYELLQHI LGGELQRKIM EVELSVHGVT HQEAQTALGA TGGDVVSALR NLKVDQLFHL SSRSRADATR ILEHYQWDLS AASRYV
Anfinsen_slept_here Lv 1
The first 70 residues seem to be the 2TEL crystallization module. see PDB 2QB1 amongst others. This factoid might be useful for getting started.
Skippysk8s Lv 1
:)
Susume Lv 1
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 Lv 1
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 Lv 1
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.