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- PDB-1s6x: Solution structure of VSTx -

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Basic information

Entry
Database: PDB / ID: 1s6x
TitleSolution structure of VSTx
ComponentsKvAP CHANNEL
KeywordsTOXIN / Double stranded antiparallel beta-sheet / Inhibitory cystine knot
Function / homology
Function and homology information


ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Huwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin
Similarity search - Domain/homology
Kappa-theraphotoxin-Gr3a
Similarity search - Component
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsJung, H.J. / Eu, Y.J. / Kim, J.I.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure and lipid membrane partitioning of VSTx1, an inhibitor of the KvAP potassium channel.
Authors: Jung, H.J. / Lee, J.Y. / Kim, S.H. / Eu, Y.J. / Shin, S.Y. / Milescu, M. / Swartz, K.J. / Kim, J.I.
History
DepositionJan 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KvAP CHANNEL


Theoretical massNumber of molelcules
Total (without water)4,0101
Polymers4,0101
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)20 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #7lowest energy

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Components

#1: Protein/peptide KvAP CHANNEL / VSTx / GATING MODIFIER TOXIN


Mass: 4009.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was synthesized chemically. / References: UniProt: P60980*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111PE-COSY
121DQF-COSY
1312D NOESY
1412D TOCSY
2512D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 10mM VSTx; 90% H20, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
103.5283 K
203.5300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851refinement
XwinNMR3Brukercollection
XwinNMR3Brukerprocessing
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 756 restraints, 721 are NOE derived distance constraints, 18 dihedral angle restraints, 8 distance restraints from hydrogen bonds, and 9 distance ...Details: The structures are based on a total of 756 restraints, 721 are NOE derived distance constraints, 18 dihedral angle restraints, 8 distance restraints from hydrogen bonds, and 9 distance restraints from disulfide bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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