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2234: Electron Density Reconstruction 18

Closed since over 3 years ago

Novice Overall Prediction Electron Density

Summary

Created
December 01, 2022
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.

Sequence
GFEKYWFCYGIKCYYFDMDRKTWSGCKQTCQISSLSLLKIDNEDELKFLQNLAPSDISWIGFSYDNKKKDWAWIDNGPSKLALNTTKYNIRDGLCMSLSKTRLDNGDCGKSYICICGKRLDKFPH

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Comments

horowsah Staff Lv 1

There's actually two identical copies next to each other in this one. So it's the same thing doubled.

LociOiling Lv 1

A little late, but I see AA Edit was unable to detect the two chains in this puzzle, instead showing just one chain with 248 segments. It appears the N terminals (segments 1 and 124) don't have the expected atom count.

The first chain is also missing the first two segments (G and F) stated in the puzzle description. The first chain is 123 segments, and the second chain is 125 segments. So the puzzle is not quite a dimer, since the two chains are not identical. This doesn't explain the issue with the atom counts.

Recipes can't really look at the protein, so looking at atom counts is the main way of detecting chains. That usually works, but some puzzles have non-standard atom counts. The other way for a recipe to detect chains is to look at the distance between the atom carbons of each pair of adjacent segments. This approach has its own set of problems on some puzzles that present a large protein with many segments trimmed away.

In this puzzle at least, the chain ID is shown in the segment information window. So segment 123 shows "PDB#: A 262", and segment 124 shows "PDB: B 138". So segment 123 is chain A, and segment 124 is chain B. Unfortunately, recipes can't access this information.

Anyway, here's my solution: