+Open data
-Basic information
Entry | Database: PDB / ID: 6img | ||||||
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Title | Solution Structure of Bicyclic Peptide pb-13 | ||||||
Components | (ACE)-GLY-CYS-PRO-CYS-ILE-TRP-PRO-GLU-LEU-CYS-PRO-TRP-ILE-ARG-SER-CYS-(NH2) | ||||||
Keywords | DE NOVO PROTEIN / bicyclic peptide / cystine bridge / proline rich | ||||||
Biological species | Enterobacteria phage M13 (virus) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Yao, H. / Lin, P. / Zha, J. / Zha, M. / Zhao, Y. / Wu, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Chembiochem / Year: 2019 Title: Ordered and Isomerically Stable Bicyclic Peptide Scaffolds Constrained through Cystine Bridges and Proline Turns. Authors: Lin, P. / Yao, H. / Zha, J. / Zhao, Y. / Wu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6img.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6img.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 6img.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6img_validation.pdf.gz | 340.6 KB | Display | wwPDB validaton report |
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Full document | 6img_full_validation.pdf.gz | 395.2 KB | Display | |
Data in XML | 6img_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 6img_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/6img ftp://data.pdbj.org/pub/pdb/validation_reports/im/6img | HTTPS FTP |
-Related structure data
Related structure data | 6imhC 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: Protein/peptide | ( Mass: 1888.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage M13 (virus) |
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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: 4.3 mM pb-13, acetonitrile/water Details: The peptide was dissolved in a mixture of 90% perdeuterated acetonitrile and 10% H2O (pH=1) or D2O (pD=1). Label: NA_pb13 / Solvent system: acetonitrile/water | |||||||||||||||||||||
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Sample | Conc.: 4.3 mM / Component: pb-13 / Isotopic labeling: natural abundance | |||||||||||||||||||||
Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz / Details: TCI cryoprobe |
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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: 100 / Conformers submitted total number: 20 |