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2383: Electron Density Reconstruction 67- extended deadline (Use Trim Tool!)

Closed since over 2 years ago

Novice Overall Prediction Electron Density

Summary

Created
November 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. There are several chains in this protein, some are the same, some are different from each other. One of them is just a short peptide. Given its large size, the Trim tool may be very much necessary to make progress!

Sequence
DKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVEPVDGVVLVDPEYLKERRVYVTLTCAFRYGRLTFRKDLFVANVQSFPPAKKPLTRLQERLIKKLGEHAYPFTFEIPPNLPCSVTLQPGPEDTGKACGVDYEVKAFCAENLEEKIHKRNSVRLVIRKVQYAPERPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADICLFNTAQYKCPVAMEEADDTVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLREGANREILGIIVSYKVKVKLVVSRASSDVAVELPFTLMHPKPDDIVFEDFAR VFKKATVYLGKRDFVDHLVEPVDGVVLVTLTCAFRYGRELGLTFRKDLFVAPLTRLQERLIKKLGEHAYPFTFEIPPNLPCSVTLQPGPKACGVDYEVKAFKRNSVRLVIRKVQYAPERPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADICLFNTAQYKCPVAMEEADDTVAPSSTFCKVYTLTPFLANNKRGLALDGKLKHEDTNLASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPFEDFAR QILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGA TNLIELDA

Top groups

  1. Avatar for BOINC@Poland 11. BOINC@Poland 1 pt. 97,871
  2. Avatar for VeFold 12. VeFold 1 pt. 80,905
  3. Avatar for 202302 13. 202302 1 pt. 77,796
  4. Avatar for Italiani Al Lavoro 14. Italiani Al Lavoro 1 pt. 74,410
  5. Avatar for WISE 380 Spring 21 A 15. WISE 380 Spring 21 A 1 pt. 0
  6. Avatar for Beta Folders 16. Beta Folders 1 pt. 0
  7. Avatar for Coastal Biochemistry 17. Coastal Biochemistry 1 pt. 0
  1. Avatar for Punzi Baker 3
    1. Punzi Baker 3 Lv 1
    100 pts. 115,613
  2. Avatar for Bruno Kestemont 2. Bruno Kestemont Lv 1 96 pts. 115,508
  3. Avatar for gmn 3. gmn Lv 1 91 pts. 115,061
  4. Avatar for drjr 4. drjr Lv 1 87 pts. 114,848
  5. Avatar for AlkiP0Ps 5. AlkiP0Ps Lv 1 83 pts. 114,050
  6. Avatar for grogar7 6. grogar7 Lv 1 79 pts. 113,943
  7. Avatar for Sandrix72 7. Sandrix72 Lv 1 75 pts. 113,641
  8. Avatar for christioanchauvin 8. christioanchauvin Lv 1 72 pts. 113,292
  9. Avatar for WBarme1234 9. WBarme1234 Lv 1 68 pts. 113,065
  10. Avatar for guineapig 10. guineapig Lv 1 65 pts. 112,957

Comments

LociOiling Lv 1

The term pucker covers the many spots in this puzzle where there are gaps due to missing residues. This puzzle incorrectly joins up the segments on either side of the gap. Many other puzzles manage to handle the gaps correctly, with the sides of the gap appearing to be in different chains.

This puzzle ended up with lots of straws, where two adjacent segments are over 50 Angstroms apart, when 4 Angstroms is the normal high end. The segments in a straw have terrible ideality. There are also a number of spots that are less dramatic, but still incorrectly bridge a missing residue gap.

For reference, here are the chains as they appeared for me at the end of the puzzle. The small chain D seems to be a true chain, it's separate in Foldit, and its sequence doesn't appear in any other chains.

AA Edit 3.0
Puzzle: 2383: Electron Density Reconstruction 67- extended deadline (Use Trim Tool!)
segment count = 1011
4 chains and ligands
chain A (protein), segments 1-345, length = 345
dkgtrvfkkaspngkltvylgkrdfvdhidlvepvdgvvlvdpeylkerrvyvtltcafrygrltfrkdlfvanvqsfppakkpltrlqerlikklgehaypftfeippnlpcsvtlqpgpedtgkacgvdyevkafcaenleekihkrnsvrlvirkvqyaperpqptaettrqflmsdkplhleasldkeiyyhgepisvnvhvtnntnktvkkikisvrqyadiclfntaqykcpvameeaddtvapsstfckvytltpflannrekrglaldgklkhedtnlasstllreganreilgiivsykvkvklvvsrassdvavelpftlmhpkpddivfedfar
chain B (protein), segments 346-645, length = 300
vfkkatvylgkrdfvdhlvepvdgvvlvtltcafrygrelgltfrkdlfvapltrlqerlikklgehaypftfeippnlpcsvtlqpgpkacgvdyevkafkrnsvrlvirkvqyaperpqptaettrqflmsdkplhleasldkeiyyhgepisvnvhvtnntnktvkkikisvrqyadiclfntaqykcpvameeaddtvapsstfckvytltpflannkrglaldgklkhedtnlasstllreganreilgiivsykvkvklvvsrggllgdlassdvavelpftlmhpkpfedfar
chain C (protein), segments 646-1003, length = 358
qilpirfqehlqlqnlginpanigfstltmesdkficirekvgeqaqvviidmndpsnpirrpisadsaimnpaskvialkagktlqifniemkskmkahtmtddvtfwkwislntvalvtdnavyhwsmegesqpvkmfdrhsslagcqiinyrtdakqkwllltgisaqqnrvvgamqlysvdrkvsqpieghaasfaqfkmegnaeestlfcfavrgqaggklhiievgtpptgnqpfpkkavdvffppeaqndfpvamqisekhdvvflitkygyihlydletgtciymnrisgetifvtapheatagiigvnrkgqvlsvcveeeniipyitnvlqnpdlalrmavrnnlaga
chain D (protein), segments 1004-1011, length = 8
tnlielda