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Yorodumi- PDB-1ryg: Three dimensional solution structure of the R29A MUTANT of sodium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ryg | ||||||
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Title | Three dimensional solution structure of the R29A MUTANT of sodium channels inhibitor HAINANTOXIN-IV by 2D 1H-NMR | ||||||
Components | Hainantoxin-IV | ||||||
Keywords | TOXIN / Neurotoxin / Inhibitor cystine knot motif | ||||||
Function / homology | Function and homology information host cell presynaptic membrane / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Li, D. / Lu, S. / Gu, X. / Liang, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure--activity relationships of hainantoxin-IV and structure determination of active and inactive sodium channel blockers Authors: Li, D. / Xiao, Y. / Xu, X. / Xiong, X. / Lu, S. / Liu, Z. / Zhu, Q. / Wang, M. / Gu, X. / Liang, S. #1: Journal: Acta Biochim.Biophys.Sinica / Year: 2002 Title: Synthesis and Oxidative Refolding of Hainantoxin-Iv Authors: Liu, Z.H. / Chen, P. / Liang, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ryg.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ryg.ent.gz | 178 KB | Display | PDB format |
PDBx/mmJSON format | 1ryg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/1ryg ftp://data.pdbj.org/pub/pdb/validation_reports/ry/1ryg | HTTPS FTP |
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-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: 3913.513 Da / Num. of mol.: 1 / Mutation: R29A / Source method: obtained synthetically / Details: synthesized using standard fmoc chemistry. / References: UniProt: P83471, UniProt: D2Y232*PLUS |
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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. |
-Sample preparation
Details | Contents: 5.0mM Solvent system: 20mM deuterium acetic acid BU, 90% H2O, 10% D2O |
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Sample conditions | Ionic strength: 20 / pH: 4.00 / Pressure: 1 atm / Temperature: 295 K |
-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: simulated annealing / Software ordinal: 1 Details: the structures are based on 366 NOE- derived distance constraints, 15 dihedral angle restraints, 9 fake distance restraints from disulfide bonds and 12 hydrogen- bond constrains. | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |