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Yorodumi- PDB-8cto: Solution NMR structure of 8-residue Rosetta-designed cyclic pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cto | ||||||
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Title | Solution NMR structure of 8-residue Rosetta-designed cyclic peptide D8.31 in d6-DMSO with cis/trans switching (B-CT conformation) | ||||||
Components | Cyclic peptide D8.31 DAL-DPR-MLU-DVA-DAL-DPR-MLU-DVA | ||||||
Keywords | DE NOVO PROTEIN / cyclic peptide / non natural amino acids / cis/trans / switch peptides / de novo design / membrane permeability | ||||||
Function / homology | polypeptide(D) Function and homology information | ||||||
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 | 8cto.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cto.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 8cto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cto_validation.pdf.gz | 282.8 KB | Display | wwPDB validaton report |
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Full document | 8cto_full_validation.pdf.gz | 289.2 KB | Display | |
Data in XML | 8cto_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 8cto_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8cto ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8cto | HTTPS FTP |
-Related structure data
Related structure data | 7ubcC 7ubdC 7ubeC 7ubfC 7ubgC 7ubhC 7ubiC 7ucpC 7uzlC 8cunC 8cwaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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: Polypeptide(D) | Mass: 807.030 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, DMSO / Details: D8.31-DMSO / Label: peptide / Solvent system: DMSO | ||||||||||||
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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 | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 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 B (CT) of the 8-residue cyclic peptide present in the same NMR sample in d6-DMSO. A-CC conformation (50%) has cis MLU-3 and cis MLU-7 (pdb 7UBD) and B-CT (50%) ...Details: This is conformation B (CT) of the 8-residue cyclic peptide present in the same NMR sample in d6-DMSO. A-CC conformation (50%) has cis MLU-3 and cis MLU-7 (pdb 7UBD) and B-CT (50%) conformation has cis MLU-3 and trans MLU-7 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: medoid | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |