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- PDB-1wqk: Solution structure of APETx1, a specific peptide inhibitor of hum... -

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Basic information

Entry
Database: PDB / ID: 1wqk
TitleSolution structure of APETx1, a specific peptide inhibitor of human Ether-a-go-go-related gene potassium channels from the venom of the sea anemone Anthopleura elegantissima: a new fold for an HERG toxin
ComponentsToxin APETx1
KeywordsTOXIN / Anthopleura elegantissima / sea anemone toxin / structure determination / potassium channel inhibitor / APETx1 / HERG
Function / homology
Function and homology information


nematocyst / ion channel inhibitor activity / potassium channel regulator activity / sodium channel regulator activity / toxin activity / defense response to bacterium / extracellular region
Similarity search - Function
BDS potassium channel toxin / Potassium-channel blocking toxin / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Kappa-actitoxin-Ael2a
Similarity search - Component
Biological speciesAnthopleura elegantissima (clonal anemone)
MethodSOLUTION NMR
AuthorsChagot, B. / Diochot, S. / Pimentel, C. / Lazdunski, M. / Darbon, H.
CitationJournal: Proteins / Year: 2005
Title: Solution structure of APETx1 from the sea anemone Anthopleura elegantissima: A new fold for an HERG toxin
Authors: Chagot, B. / Diochot, S. / Pimentel, C. / Lazdunski, M. / Darbon, H.
History
DepositionSep 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin APETx1


Theoretical massNumber of molelcules
Total (without water)4,5611
Polymers4,5611
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)25 / 50structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: Protein/peptide Toxin APETx1


Mass: 4561.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Anthopleura elegantissima (clonal anemone)
References: UniProt: P61541

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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NMR measurement

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

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Processing

NMR software
NameVersionClassification
XwinNMR2.1collection
XEASY1.3.13data analysis
ARIA1.2refinement
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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