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Yorodumi- PDB-7ubg: Solution NMR structure of 9-residue Rosetta-designed cyclic pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ubg | ||||||
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Title | Solution NMR structure of 9-residue Rosetta-designed cyclic peptide D9.16 in CDCl3 with cis/trans switching (A-TT conformation) | ||||||
Components | Cyclic peptide D9.16 DPR-MAA-ALA-DVA-MLE-LEU-LEU-PRO-DLE | ||||||
Keywords | DE NOVO PROTEIN / cyclic peptide / non natural amino acids / cis/trans / switch peptides / de novo design / membrane permeability | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / na | ||||||
Authors | Ramelot, T.A. / Tejero, R. / Montelione, G.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ubg.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ubg.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ubg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ubg_validation.pdf.gz | 370.6 KB | Display | wwPDB validaton report |
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Full document | 7ubg_full_validation.pdf.gz | 444.7 KB | Display | |
Data in XML | 7ubg_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 7ubg_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/7ubg ftp://data.pdbj.org/pub/pdb/validation_reports/ub/7ubg | HTTPS FTP |
-Related structure data
Related structure data | 7ubcC 7ubdC 7ubeC 7ubfC 7ubhC 7ubiC 7ucpC 7uzlC 8ctoC 8cunC 8cwaC C: citing same article (ref.) |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 934.215 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
Details | Type: solution / Contents: 6 mg/mL peptide, 0.03 % TMS, chloroform / Details: D9.16-CDCl3 / Label: peptide / Solvent system: chloroform | ||||||||||||
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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 / Pressure err: 0.1 / Temperature: 293 K / Temperature err: 1 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz / Details: CP-TCI-Pharaoh - RPI |
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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 9-residue cyclic peptide present in the same NMR sample in CDCl3. TT conformation has trans DPR-1 and trans DPR-8. TC conformation has trans DPR-1 and ...Details: This is conformation A (TT) of the same 9-residue cyclic peptide present in the same NMR sample in CDCl3. TT conformation has trans DPR-1 and trans DPR-8. TC conformation has trans DPR-1 and cis DPR-8a (pdb 7UZL) | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: medoid | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |