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- PDB-2ky3: Solution structure of GS-alfa-Ktx5.4 synthetic scorpion like -

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Basic information

Entry
Database: PDB / ID: 2ky3
TitleSolution structure of GS-alfa-Ktx5.4 synthetic scorpion like
ComponentsPotassium channel toxin alpha-KTx 5.4
KeywordsTOXIN / alpha/beta scaffold / beta sheet / alpha helix / scoprion K+ toxin / GS-alpha-Ktx5.4 / aKtx5.4 / Mesobuthus tamulus / potassium blocker
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 / TORSION ANGLE DYNAMICS, MOLECULAR DYNAMICS
Model detailslowest energy, model 1
AuthorsDel Rio-Portilla, F. / Ramirez-Cordero, B.E. / Brieba-De Castro, L.
Citation
Journal: 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.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Tamapin, a venom peptide from the Indian red scorpion (Mesobuthus tamulus) that targets small conductance Ca2+-activated K+ channels and afterhyperpolarization currents in central neurons.
Authors: Pedarzani, P. / D'hoedt, D. / Doorty, K.B. / Wadsworth, J.D. / Joseph, J.S. / Jeyaseelan, K. / Kini, R.M. / Gadre, S.V. / Sapatnekar, S.M. / Stocker, M. / Strong, P.N.
History
DepositionMay 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Jul 2, 2014Group: Database references
Revision 1.4Oct 8, 2014Group: Database references
Revision 1.5Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 5.4


Theoretical massNumber of molelcules
Total (without water)3,6141
Polymers3,6141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 200target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 3614.315 Da / Num. of mol.: 1
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 DE3 gami / References: UniProt: P59869

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

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Sample preparation

DetailsContents: 1.8 mM GS-alfa-Ktx5.4 SCORPION TOXIN, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1.8 mM / Component: GS-alfa-Ktx5.4 SCORPION TOXIN-1
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 297 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
VARIAN INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
XEASY_MOLMOL_2K.22K.2Bartels et al.chemical shift assignment
PROCHECK3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOL2k.2Koradi, Billeter and Wuthrichdata analysis
RefinementMethod: TORSION ANGLE DYNAMICS, MOLECULAR DYNAMICS / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 17

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