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- PDB-2lu9: NMR solution structure of recombinant Tamapin -

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Basic information

Entry
Database: PDB / ID: 2lu9
TitleNMR solution structure of recombinant Tamapin
ComponentsPotassium channel toxin alpha-KTx 5.4
KeywordsTOXIN / CS alpha beta
Function / homologyScorpion 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 speciesMesobuthus tamulus (Indian red scorpion)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Authorsdel Rio-Portilla, F. / Ramirez-Cordero, B.
CitationJournal: Chem.Res.Toxicol. / Year: 2014
Title: Cytotoxicity of recombinant tamapin and related toxin-like peptides on model cell lines.
Authors: Ramirez-Cordero, B. / Toledano, Y. / Cano-Sanchez, P. / Hernandez-Lopez, R. / Flores-Solis, D. / Saucedo-Yanez, A.L. / Chavez-Uribe, I. / Brieba, L.G. / Del Rio-Portilla, F.
History
DepositionJun 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 5.4


Theoretical massNumber of molelcules
Total (without water)3,4701
Polymers3,4701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 200structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 5.4 / Tamapin


Mass: 3470.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus tamulus (Indian red scorpion)
References: UniProt: P59869
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQFCOSY
121TOCSY
131NOESY
141NOESY

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Sample preparation

DetailsContents: 0.8 mM recombinant-tamapin, 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.8 mM / Component: recombinant-tamapin-1
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Inova / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 18

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