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- PDB-7zru: Solution structure of Pi6, a low affinity blocking kappa-K+-chann... -

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Basic information

Entry
Database: PDB / ID: 7zru
TitleSolution structure of Pi6, a low affinity blocking kappa-K+-channel peptide from the scorpion Pandinus imperator
ComponentsPotassium channel toxin kappa-KTx 2.9
KeywordsTOXIN / scorpion toxin potassium channel blocker
Function / homologynegative regulation of voltage-gated potassium channel activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin kappa-KTx 2.9
Function and homology information
Biological speciesPandinus imperator (emperor scorpion)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDelepierre, M. / Olamendi Portugal, T. / Possani, L.D. / Guijarro, J.I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Not Published
Title: Not applicable
Authors: guijarro, J.I.
History
DepositionMay 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 16, 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin kappa-KTx 2.9


Theoretical massNumber of molelcules
Total (without water)3,1351
Polymers3,1351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Potassium channel toxin kappa-KTx 2.9 / Potassium channel-blocking toxin 6 / Pi6


Mass: 3134.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pandinus imperator (emperor scorpion) / Organ: venom gland / References: UniProt: C0HKB3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 0.19 mM pi6, 90% H2O/10% D2O / Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.19 mM / Component: pi6 / Isotopic labeling: none
Sample conditionsIonic strength: 0 mM / Label: 1 / pH: 4 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpin4.1Bruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structure ensemble is based on a total of 332 restraints, of which 309 are NOE derived distance restraints, 11 are hydrogen bonds and 12 are phi angle dihedral restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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