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2344: Electron Density Reconstruction 54 (Trim tool recommended)

Closed since over 2 years ago

Novice Overall Prediction Electron Density

Summary

Created
August 21, 2023
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 one has a big protein chain and then two smaller protein chains as well. Also, it's pretty gigantic, so the Trim Tool is highly recommended.

Sequence
KKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWGRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLREKVSELHPAIAKL TDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYIKGILK ETFSKIRVKPEHVIGVTVAFVIIEAILTYGRF

Top groups

  1. Avatar for Go Science
    1. Go Science
    100 pts. 50,511
  2. Avatar for Anthropic Dreams 2. Anthropic Dreams 60 pts. 50,062
  3. Avatar for L'Alliance Francophone 3. L'Alliance Francophone 33 pts. 49,739
  4. Avatar for Contenders 4. Contenders 17 pts. 49,540
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  6. Avatar for FamilyBarmettler 6. FamilyBarmettler 4 pts. 48,644
  7. Avatar for Marvin's bunch 7. Marvin's bunch 2 pts. 47,567
  8. Avatar for BOINC@Poland 8. BOINC@Poland 1 pt. 46,234
  9. Avatar for Gargleblasters 9. Gargleblasters 1 pt. 44,878
  10. Avatar for VeFold 10. VeFold 1 pt. 44,555
  1. Avatar for Deleted player 41. Deleted player 1 pt. 45,491
  2. Avatar for Joanna_H 42. Joanna_H Lv 1 1 pt. 44,878
  3. Avatar for Dr.Sillem 43. Dr.Sillem Lv 1 1 pt. 44,555
  4. Avatar for rinze 44. rinze Lv 1 1 pt. 44,339
  5. Avatar for nicobul 45. nicobul Lv 1 1 pt. 44,300
  6. Avatar for DScott 46. DScott Lv 1 1 pt. 44,248
  7. Avatar for froschi2 47. froschi2 Lv 1 1 pt. 44,125
  8. Avatar for pfirth 48. pfirth Lv 1 1 pt. 43,799
  9. Avatar for Mohoernchen 49. Mohoernchen Lv 1 1 pt. 43,682
  10. Avatar for hansvandenhof 50. hansvandenhof Lv 1 1 pt. 43,578

Comments

Artoria2e5 Lv 1

This is the SecYEG translocon of Methanocaldococcus jannaschii. There are multiple PDB structures of this complex and I don't know which one this is.

AA Edit dumps

>A
kklipilekipevelpvkeitfkeklkwtgivlvlyfimgcidvytagaqipaifefwgrigtlitlgigpivtagiimqllvgsgiiqmdlsipenralfqgcqkllsiimcfveavlfvgagafgiltpllaflviiqiafgsiiliyldeivskygigsgiglfiaagvsqtifvgalgpegylwkflnsliqgvpnieyiapiigtiivflmvvyaecmrveiplahgrikgavgkypikfvyvsnipvilaaalfaniqlwglalyrmgipilghyeggravdgiayylstpyglssvisdpihaivymiamiitcvmfgifwvettgldpksmakrigslgmaikgfrksekaiehrlkryippltvmssafvgflatianfigalgggtgvlltvsivyrmyeqllrekvselhpaiakl
>B
tdfnqkieqlkefieecrrvwlvlkkptkdeylavakvtalgisllgiigyiihvpatyikgilk
>C
etfskirvkpehvigvtvafviieailtygrf

Blasting A gives an exact match at 2YXQ, which has no unmodelled residues in-between. Good!

Oh, and don't worry too much about burials. A good chunk of this thing sits in a lipid membrane.