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2663: Electron Density Reconstruction 136

Closed since 6 months ago

Novice Overall Prediction Electron Density

Summary

Created
September 10, 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. This puzzle has four copies of the same small protein, but not all the segments that are visible are the same.

Sequence
MVRANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTNKKRPAATERSEQIQMEF

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Comments

LociOiling Lv 1

The puzzle is live now, and it looks like 1ZPQ is a good match, based on the missing residues.

The link for 1ZPQ goes to the structure tab of the PDB page. It shows the sequence at the top of the display, starting with chain A. Any missing residues are greyed out. A dropdown lets you change the chain displayed.

AA Edit 3.0 shows the chains as they are found in the puzzle. That can be compared to what's shown on the structure tab.

For this puzzle, all four chains appear to have the same sequence, but the number of missing residues at the beginning and end is different for each. All together, the pattern of missing residues gives a unique fingerprint (probably unique, at least) that helps confirm a match between PDB and puzzle.

Here's what the display for chain C shows, with the missing residues highlighted in red:

Here's the dropdown or twirly in action:

LociOiling Lv 1

Here's a manual alignment of the FASTA sequence (Display Files -> FASTA Sequence) for 1ZPQ and the AA Edit 3.0 output for puzzle 2663:

The PDB info is in uppercase, the AA Edit output is in lowercase. The PDB shows the same sequence for all four chains, so I just repeated that line four times.