+Open data
-Basic information
Entry | Database: PDB / ID: 2ndb | ||||||
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Title | NMR structure of omega-agatoxin IVA in DPC micelles | ||||||
Components | Omega-agatoxin-Aa4a | ||||||
Keywords | TOXIN / NEUROTOXIN | ||||||
Function / homology | Function and homology information host cell presynaptic membrane / calcium channel inhibitor activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Agelenopsis aperta (spider) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model14 | ||||||
Authors | Ryu, J.H. / Kim, J.I. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structure-activity relationships of omega-Agatoxin IVA in lipid membranes Authors: Ryu, J.H. / Jung, H.J. / Konishi, S. / Kim, H.H. / Park, Z.Y. / Kim, J.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ndb.cif.gz | 284.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ndb.ent.gz | 238.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ndb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/2ndb ftp://data.pdbj.org/pub/pdb/validation_reports/nd/2ndb | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5277.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agelenopsis aperta (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P30288 |
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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: 50 mM [U-100% 2H] DPC-1, d38-DPC / Solvent system: d38-DPC |
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Sample | Conc.: 50 mM / Component: DPC-1 / Isotopic labeling: [U-100% 2H] |
Sample conditions | pH: 4.0 / Pressure: ambient / Temperature: 310 |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle 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 / Representative conformer: 14 |