+Open data
-Basic information
Entry | Database: PDB / ID: 6bes | ||||||
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Title | Solution structure of de novo macrocycle design11_ss | ||||||
Components | (DAL)Q(DPR)(DCY)(DLY)DS(DTY)(DCY)P(DSN) | ||||||
Keywords | DE NOVO PROTEIN / macrocycle / de novo | ||||||
Function / homology | polypeptide(D) / polypeptide(D) (> 10) Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Shortridge, M.D. / Hosseinzadeh, P. / Pardo-Avila, F. / Varani, G. / Baker, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2017 Title: Comprehensive computational design of ordered peptide macrocycles. Authors: Hosseinzadeh, P. / Bhardwaj, G. / Mulligan, V.K. / Shortridge, M.D. / Craven, T.W. / Pardo-Avila, F. / Rettie, S.A. / Kim, D.E. / Silva, D.A. / Ibrahim, Y.M. / Webb, I.K. / Cort, J.R. / ...Authors: Hosseinzadeh, P. / Bhardwaj, G. / Mulligan, V.K. / Shortridge, M.D. / Craven, T.W. / Pardo-Avila, F. / Rettie, S.A. / Kim, D.E. / Silva, D.A. / Ibrahim, Y.M. / Webb, I.K. / Cort, J.R. / Adkins, J.N. / Varani, G. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bes.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bes.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bes_validation.pdf.gz | 356.1 KB | Display | wwPDB validaton report |
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Full document | 6bes_full_validation.pdf.gz | 372.4 KB | Display | |
Data in XML | 6bes_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6bes_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/6bes ftp://data.pdbj.org/pub/pdb/validation_reports/be/6bes | HTTPS FTP |
-Related structure data
Related structure data | 6be7C 6be9C 6benC 6beoC 6beqC 6berC 6betC 6beuC 6bewC 6bf3C 6bf5C C: citing same article (ref.) |
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Similar structure data | |
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: 1198.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 5 mg/mL Design 11_ss, 5 % v/v [U-99% 2H] glycerol, 90% H2O/10% D2O Label: 11cpp_1 / Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 Not defined / Label: cond_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 278 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |