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Yorodumi- PDB-1jbf: Hairpin Peptide that Inhibits IgE Activity by Binding to the High... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jbf | ||||||
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Title | Hairpin Peptide that Inhibits IgE Activity by Binding to the High Affinity IgE Receptor | ||||||
Components | IGE06 | ||||||
Keywords | PROTEIN BINDING / beta-hairpin / type I turn | ||||||
Method | SOLUTION NMR / Hybrid distance geometry, simulated annealing, restrained molecular dynamics. | ||||||
Authors | Nakamura, G.R. / Starovasnik, M.A. / Reynolds, M.E. / Lowman, H.B. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: A novel family of hairpin peptides that inhibit IgE activity by binding to the high-affinity IgE receptor. Authors: Nakamura, G.R. / Starovasnik, M.A. / Reynolds, M.E. / Lowman, H.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jbf.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jbf.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jbf ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jbf | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 1776.090 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was chemically synthesized. It was based on naive phage-peptide library sorted for binding IgE receptor |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: 3JHNHa were obtained by fitting Lorentzian lines to the antiphase doublets of HN-Ha peaks in a 2QF-COSY spectrum processed to high digital resolution in F2. 3JHNHa for Gly8 and Gly11 were ...Text: 3JHNHa were obtained by fitting Lorentzian lines to the antiphase doublets of HN-Ha peaks in a 2QF-COSY spectrum processed to high digital resolution in F2. 3JHNHa for Gly8 and Gly11 were obtained from analysis of the COSY-35 spectrum acquired in H2O. 3JHaHb were extracted from a COSY-35 spectrum acquired in D2O. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: no salt / pH: 5.7 / Pressure: ambient / Temperature: 288 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: Hybrid distance geometry, simulated annealing, restrained molecular dynamics. Software ordinal: 1 Details: Structures were calculated based on a total of 109 distance and 16 dihedral angle restraints. The final ensemble of 20 models has no distance or dihedral angle restraint violations greater ...Details: Structures were calculated based on a total of 109 distance and 16 dihedral angle restraints. The final ensemble of 20 models has no distance or dihedral angle restraint violations greater than 0.1 angstrom or 2 degrees, respectively. | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 20 |