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Yorodumi- PDB-1y29: Three dimensional solution structure of huwentoxin-x by 2D 1H-NMR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y29 | ||||||
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Title | Three dimensional solution structure of huwentoxin-x by 2D 1H-NMR | ||||||
Components | huwentoxin-x | ||||||
Keywords | TOXIN / A double-stranded beta-sheet / ICK / Knottin | ||||||
Function / homology | toxin activity / extracellular region / Omega-theraphotoxin-Hs1a Function and homology information | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Liu, Z. / Liang, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Function and solution structure of Huwentoxin-X, a specific blocker of N-type calcium channels, from the Chinese bird spider Ornithoctonus huwena Authors: Liu, Z. / Dai, J. / Dai, L. / Deng, M. / Hu, Z. / Hu, W. / Liang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y29.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y29.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 1y29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/1y29 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/1y29 | 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: 2942.567 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was isolated from the venom of spider Ornithoctonus huwena, synthesized by using solid phase chemical method. References: UniProt: P68424 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 5MM HUWENTOXIN-X; PHOSPHATE BUFFER / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20 / pH: 4.5 / Pressure: 1 atm / Temperature: 298 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 DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing / Software ordinal: 1 Details: The structures are based on 261 noe-derived distance constraints, 10 dihedral angel restraints and 9 fake distance restraints from disulfide bonds. | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |