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- PDB-1scy: DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF SCYLLATOXIN B... -

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Basic information

Entry
Database: PDB / ID: 1scy
TitleDETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF SCYLLATOXIN BY 1H NUCLEAR MAGNETIC RESONANCE
ComponentsSCYLLATOXIN
KeywordsNEUROTOXIN
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 5.1
Function and homology information
Biological speciesLeiurus quinquestriatus hebraeus (scorpion)
MethodSOLUTION NMR
AuthorsMartins, J.C. / Van De Ven, F.J.M. / Borremans, F.A.M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Determination of the three-dimensional solution structure of scyllatoxin by 1H nuclear magnetic resonance.
Authors: Martins, J.C. / Van de Ven, F.J. / Borremans, F.A.
#1: Journal: FEBS Lett. / Year: 1990
Title: Solution Conformation of Leiurotoxin I (Scyllatoxin) by 1H Nuclear Magnetic Resonance. Resonance Assignment and Secondary Structure
Authors: Martins, J.C. / Zhang, W. / Tartar, A. / Lazdunski, M. / Borremans, F.A.M.
History
DepositionJun 2, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCYLLATOXIN


Theoretical massNumber of molelcules
Total (without water)3,4341
Polymers3,4341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: CYS 21 - ILE 22 MODEL 2 OMEGA = 149.70 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA 1 - PHE 2 MODEL 6 OMEGA = 211.28 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ASP 24 - LYS 25 MODEL 6 OMEGA = 229.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CYS 21 - ILE 22 MODEL 7 OMEGA = 146.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: ASP 24 - LYS 25 MODEL 8 OMEGA = 230.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: GLY 19 - LYS 20 MODEL 10 OMEGA = 219.59 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: ASP 24 - LYS 25 MODEL 12 OMEGA = 214.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: LYS 20 - CYS 21 MODEL 16 OMEGA = 213.91 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: LYS 20 - CYS 21 MODEL 20 OMEGA = 214.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: ASP 24 - LYS 25 MODEL 21 OMEGA = 213.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: ALA 1 - PHE 2 MODEL 22 OMEGA = 228.55 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: CYS 3 - ASN 4 MODEL 25 OMEGA = 145.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / -
Representative

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Components

#1: Protein/peptide SCYLLATOXIN


Mass: 3434.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leiurus quinquestriatus hebraeus (scorpion)
Species: Leiurus quinquestriatus / Strain: hebraeus / References: UniProt: P16341
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameDeveloperClassification
DIANAGUNTERT,BRAUN,WUTHRICHrefinement
AmberPEARLMAN,CASE,CALDWELL,SIEBEL,SINGH,WEINER,KOLLMANrefinement
NMR ensembleConformers submitted total number: 25

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