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- PDB-5wlx: Solution structure of kappa-theraphotoxin-Aa1a -

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Basic information

Entry
Database: PDB / ID: 5wlx
TitleSolution structure of kappa-theraphotoxin-Aa1a
ComponentsKappa-theraphotoxin-Aa1a
KeywordsTOXIN / Spider toxins / Inhibitor cystine knot / Theraphotoxin
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Kappa-theraphotoxin-Aa1a
Function and homology information
Biological speciesAvicularia (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.Y. / Ma, L. / King, G.F.
CitationJournal: Biochem. Pharmacol. / Year: 2018
Title: Novel venom-derived inhibitors of the human EAG channel, a putative antiepileptic drug target.
Authors: Ma, L. / Chin, Y.K.Y. / Dekan, Z. / Herzig, V. / Chow, C.Y. / Heighway, J. / Lam, S.W. / Guillemin, G.J. / Alewood, P.F. / King, G.F.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3Oct 30, 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: Kappa-theraphotoxin-Aa1a


Theoretical massNumber of molelcules
Total (without water)4,1641
Polymers4,1641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area3150 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200Best stereochemical properties as judged by Molprobity
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Kappa-theraphotoxin-Aa1a


Mass: 4163.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Avicularia (spider) / References: UniProt: A0A3F2YLP5*PLUS
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
111anisotropic12D 1H-15N HSQC
121anisotropic12D 1H-13C HSQC
131anisotropic12D 1H-1H TOCSY
141anisotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM Kappa-theraphotoxin-Aa1a, 20 mM sodium phosphate, 95% H2O/5% D2O
Label: p31 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKappa-theraphotoxin-Aa1anatural abundance1
20 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 20 mM / Label: p31 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker B / Manufacturer: Bruker / Model: B / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Best stereochemical properties as judged by Molprobity
Conformers calculated total number: 200 / Conformers submitted total number: 20

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