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- PDB-7ubf: Solution NMR structure of 8-residue Rosetta-designed cyclic pepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ubf | ||||||
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Title | Solution NMR structure of 8-residue Rosetta-designed cyclic peptide D8.21 in 50% d6-DMSO and 50% water with cis/trans switching (CC conformation, 50%) | ||||||
![]() | Cyclic peptide D8.21 DVA-MLE-DPR-LEU-DVA-MLE-DPR-LEU | ||||||
![]() | DE NOVO PROTEIN / cyclic peptide / non natural amino acids / cis/trans / switch peptides / de novo design / membrane permeability | ||||||
Function / homology | polypeptide(D)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / na | ||||||
![]() | Ramelot, T.A. / Tejero, R. / Montelione, G.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Accurate de novo design of membrane-traversing macrocycles. Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / ...Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / Craven, T.W. / Tejero, R. / Lauko, A. / Choi, R. / Glynn, C. / Dong, L. / Griffin, R. / van Voorhis, W.C. / Rodriguez, J. / Stewart, L. / Montelione, G.T. / Craik, D. / Baker, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52 KB | Display | ![]() |
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PDB format | ![]() | 35.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 282.7 KB | Display | ![]() |
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Full document | ![]() | 288.7 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ubcC ![]() 7ubdC ![]() 7ubeC ![]() 7ubgC ![]() 7ubhC ![]() 7ubiC ![]() 7ucpC ![]() 7uzlC ![]() 8ctoC ![]() 8cunC ![]() 8cwaC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Polypeptide(D) | Mass: 891.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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Sample conditions | Ionic strength: NA Not defined / Label: conditions_1 / pH: 0.0 Not defined / Pressure: 1 atm / Temperature: 293 K / Temperature err: 1 |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: na / Software ordinal: 1 Details: This is conformation A (TT) of the same 8-residue cyclic peptide present in the same NMR sample in 50% d6-DMSO and 50% water. TT symmetric conformation has trans DPR3 and trans DPR7 (7UBF, ...Details: This is conformation A (TT) of the same 8-residue cyclic peptide present in the same NMR sample in 50% d6-DMSO and 50% water. TT symmetric conformation has trans DPR3 and trans DPR7 (7UBF, 50%). CC symmetric conformation has cis DPR3 and cis DPR7 (50%). | ||||||||||||||||||||||||
NMR representative | Selection criteria: medoid | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |