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- PDB-1y2p: Solution structure of Hstx3P -

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Basic information

Entry
Database: PDB / ID: 1y2p
TitleSolution structure of Hstx3P
ComponentsNeurotoxin HsTX1
KeywordsTOXIN / HSTX3P / POTASSIUM CHANNEL
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 6.3
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsMosbah, A. / Gariga, L. / Darbon, H. / Sabatier, J.M.
CitationJournal: Proteins / Year: 2005
Title: The impact of the fourth disulfide bridge in scorpion toxins of the alpha-KTx6 subfamily
Authors: Carrega, L. / Mosbah, A. / Ferrat, G. / Beeton, C. / Andreotti, N. / Mansuelle, P. / Darbon, H. / De Waard, M. / Sabatier, J.M.
History
DepositionNov 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 23, 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: Neurotoxin HsTX1


Theoretical massNumber of molelcules
Total (without water)3,8371
Polymers3,8371
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 / 50target function,structures with the lowest energy,structures with the least restraint violations,structures with favorable non-bond energy,structures with acceptable covalent geometry,back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Neurotoxin HsTX1 / hstx3P


Mass: 3836.585 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. ABU19 ABU34 OF HSTX4P
References: UniProt: P59867
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
2312D TOCSY
1412D NOESY
2512D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2Mm hstx3P, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13ambient 300 K
23ambient 296 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionClassification
XwinNMR2.1processing
DYANAstructure solution
CNSrefinement
DIANAstructure solution
XEASYcollection
Procheckdata analysis
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations,structures with favorable non-bond energy,structures with acceptable ...Conformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations,structures with favorable non-bond energy,structures with acceptable covalent geometry,back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 50 / Conformers submitted total number: 20

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