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Yorodumi- PDB-1kcn: Structure of e109 Zeta Peptide, an Antagonist of the High-Affinit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kcn | ||||||
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Title | Structure of e109 Zeta Peptide, an Antagonist of the High-Affinity IgE Receptor | ||||||
Components | e109 zeta peptide | ||||||
Keywords | PROTEIN BINDING / disulfide-bonded / helical / "zeta" structure | ||||||
Method | SOLUTION NMR / hybrid distance geometry, simulated annealing, then further refined by restrained molecular dynamics | ||||||
Authors | Nakamura, G.R. / Reynolds, M.E. / Chen, Y.M. / Starovasnik, M.A. / Lowman, H.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Stable "zeta" peptides that act as potent antagonists of the high-affinity IgE receptor. Authors: Nakamura, G.R. / Reynolds, M.E. / Chen, Y.M. / Starovasnik, M.A. / 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 | 1kcn.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kcn.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kcn_validation.pdf.gz | 337.6 KB | Display | wwPDB validaton report |
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Full document | 1kcn_full_validation.pdf.gz | 383.6 KB | Display | |
Data in XML | 1kcn_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1kcn_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kcn ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kcn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2143.615 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 'solid-phase peptide synthesis of a novel peptide based on a naive phage-peptide library that was sorted for binding to the high-affinity 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: This structure was determined using standard 2D homonuclear techniques. 3JHNHA WERE OBTAINED BY FITTING LORENTZIAN LINES TO THE ANTIPHASE DOUBLETS OF HN-HA PEAKS IN A 2QF-COSY SPECTRUM ...Text: This structure was determined using standard 2D homonuclear techniques. 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. 3JHAHB WERE EXTRACTED FROM A COSY-35 SPECTRUM ACQUIRED IN D2O |
-Sample preparation
Details |
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Sample conditions | pH: 5.4 / 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 DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: hybrid distance geometry, simulated annealing, then further refined by restrained molecular dynamics Software ordinal: 1 Details: The structures are based on a total of 101 NOE-derived distance restraints, 18 dihedral angle restraints, and 12 distant restraints from 6 hydrogen bonds. | ||||||||||||||||||||
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 |