+Open data
-Basic information
Entry | Database: PDB / ID: 6d8u | ||||||
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Title | NMR solution structure of tamapin, mutant K20E | ||||||
Components | Potassium channel toxin alpha-KTx 5.4 | ||||||
Keywords | TOXIN / Tamapin mutant / K20E / CSalpha/beta / SK channels | ||||||
Function / homology | Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 5.4 Function and homology information | ||||||
Biological species | Mesobuthus tamulus (Indian red scorpion) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | del Rio Portilla, F. / Melchor Meneses, C.M. / Titaux Delgado, G.A. / Mayorga Flores, M. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Novel Blocker of Onco SK3 Channels Derived from Scorpion Toxin Tamapin and Active against Migration of Cancer Cells Authors: Flores, M. / Chantome, A. / Melchor-Meneses, C.M. / Domingo, I. / Titaux Delgado, G.A. / Galindo-Murillo, R. / Vandier, C. / del Rio Portilla, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d8u.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d8u.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 6d8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/6d8u ftp://data.pdbj.org/pub/pdb/validation_reports/d8/6d8u | HTTPS FTP |
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-Related structure data
Related structure data | 6d3tC 6d8hC 6d8qC 6d8rC 6d8sC 6d8tC 6d8yC 6d93C 6d9oC 6d9pC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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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: 3470.119 Da / Num. of mol.: 1 / Mutation: K20E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesobuthus tamulus (Indian red scorpion) Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P59869 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 2.0 mM Potassium channel toxin alpha-KTx 5.4, 95% H2O/5% D2O Label: 1H_sample / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 2.0 mM / Component: Potassium channel toxin alpha-KTx 5.4 / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 0 Not defined / Label: 1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 / Details: used also for simulated annealing | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |