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- PDB-1qky: Solution structure of PI7, a non toxic peptide isolated from the ... -

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Basic information

Entry
Database: PDB / ID: 1qky
TitleSolution structure of PI7, a non toxic peptide isolated from the scorpion Pandinus Imperator.
ComponentsTOXIN 7 FROM PANDINUS IMPERATOR
KeywordsNEUROTOXIN
Function / homologyScorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 6.5
Function and homology information
Biological speciesPANDINUS IMPERATOR (emperor scorpion)
MethodSOLUTION NMR / simulated annealing
AuthorsDelepierre, M. / Prochnicka-Chalufour, A. / Boisbouvier, J. / Possani, L.D.
Citation
Journal: Biochemistry / Year: 1999
Title: Pi7, an orphan peptide from the scorpion Pandinus imperator: a 1H-NMR analysis using a nano-NMR Probe.
Authors: Delepierre, M. / Prochnicka-Chalufour, A. / Boisbouvier, J. / Possani, L.D.
#1: Journal: Toxicon / Year: 1998
Title: Two Similar Peptides from the Venom of the Scorpion Pandinus Imperator, One Highly Effective Blocker and the Other Inactive on K+ Channels
Authors: Olamendi-Portugal, T. / Gomez-Lagunas, F. / Gurrola, G.B. / Possani, L.D.
History
DepositionAug 17, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Database references / Other / Category: citation / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_cs
Revision 1.4Nov 20, 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 / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TOXIN 7 FROM PANDINUS IMPERATOR


Theoretical massNumber of molelcules
Total (without water)4,2971
Polymers4,2971
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)14 / 200LEAST RESTRAINT VIOLATION, STRUCTURE QUALITY ACCORDING TO PROCHECK
RepresentativeModel #1

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Components

#1: Protein/peptide TOXIN 7 FROM PANDINUS IMPERATOR / PI7


Mass: 4297.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PANDINUS IMPERATOR (emperor scorpion) / Secretion: VENOM / References: UniProt: P58490*PLUS
Has protein modificationY
Sequence detailsTHE PEPTIDE STUDIED HERE IS RELATED IN SEQUENCE TO THE POTASSIUM CHANNEL BLOCKING TOXINS, HOWEVER ...THE PEPTIDE STUDIED HERE IS RELATED IN SEQUENCE TO THE POTASSIUM CHANNEL BLOCKING TOXINS, HOWEVER THE ALIGNMENT IS ONLY 60 PERCENT FOR THE PEPTIDES: SCKA_PANIM P55927 (47 AA) SCKB_PANIM P55928 (35 AA) SCKG_PANIM Q10726 (35 AA) 1QKY DEAIRCTGTKDCYIPCRYITGCFNSRCINKSCKCYGCT SCKA_PANIM: RGSVDYKDDDDKTISCTNPKQCYPHCKKETGYPNAKCMNRKCKCFGR SCKB_PANIM: TISCTNEKQCYPHCKKETGYPNAKCMNRKCKCFGR SCKG_PANIM LVKCRGTSDCGRPCQQQTGCPNSKCINRMCKCYGC * * * * * *

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY
NMR detailsText: THE STRUCTURE OF THE NATURAL TOXIN EXTRACTED FROM THE SCORPION VENOM WAS DETERMINED BY HOMONUCLEAR NMR AT 500 MHZ FROM NANOMOLE AMOUNT OF COMPOUND.

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Sample preparation

DetailsContents: H2O/D2O
Sample conditionspH: 3.5 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER,WUTHRICHrefinement
DYANAstructure solution
OPALstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURE WAS CALCULATED USING THE PROGRAM DYANA. TWENTY FIVE BEST DYANA CONFORMERS WERE SUBMITTED TO RESTRAINED ENERGY MINIMIZATION IN A SHELL OF 584 WATER MOLECULES USING THE PROGRAM ...Details: THE STRUCTURE WAS CALCULATED USING THE PROGRAM DYANA. TWENTY FIVE BEST DYANA CONFORMERS WERE SUBMITTED TO RESTRAINED ENERGY MINIMIZATION IN A SHELL OF 584 WATER MOLECULES USING THE PROGRAM OPAL. COORDINATES FOR THE WATER ARE NOT CONTAINED IN THIS ENTRY. FOR FURTHER DETAILS ON THE REFINEMENT SEE THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, STRUCTURE QUALITY ACCORDING TO PROCHECK
Conformers calculated total number: 200 / Conformers submitted total number: 14

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