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2630: Electron Density Reconstruction 125

Closed since 8 months ago

Novice Overall Prediction Electron Density

Summary

Created
June 26, 2025
Expires
Max points
100
Description

The structure of this protein has already been solved and published, but close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model. There's three separate protein chains here, one really big one and two smaller, so the Trim tool is recommended.

Sequence
MKKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQTITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLRERTSELHPAIAKLLNK MKTDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYIKGILKPPTTPRV MSKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILTYGRFL

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Comments

LociOiling Lv 1

This puzzle is a good match for PDB 1RH5. The amino acid sequence also matches PDB 1RHZ and others.

Although the description mentions three chains, AA Edit 3.0 and related recipes will report four chains. This is because chain A has 12 missing residues, amino acids that weren't located in the experimental data. This puzzle handles the missing residues correctly, by not connecting the sides of the gap. At segment 348, there's a gap, then segment 349 starts what the recipes call chain B (really the end of chain A).

The gap in chain A corresponds to the results for PDB 1RH5. While PDB 1RHZ has the same sequence, it doesn't have the same gap in chain A.

Some previous puzzles connected the sides of a missing residue gap with a peptide bond, which created a "pucker" with high negative ideality. The presence of puckers made the scientific results questionable, since the pucker tended to pull many adjacent segments out of position.

No puckers in 2630!