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- PDB-1f3k: THREE-DIMENSIONAL SOLUTION STRUCTURE OF OMEGA-CONOTOXIN TXVII, AN... -

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Basic information

Entry
Database: PDB / ID: 1f3k
TitleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF OMEGA-CONOTOXIN TXVII, AN L-TYPE CALCIUM CHANNEL BLOCKER
ComponentsOMEGA-CONOTOXIN TXVII
KeywordsTOXIN / OMEGA-CONOTOXIN / CYSTINE KNOT MOTIF / TRIPLE-STRANDED ANTIPARALLEL BETA-SHEET / L-TYPE CALCIUM CHANNEL BLOCKER
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, omega-type, conserved site / Omega-conotoxin family signature. / Conotoxin / Conotoxin
Similarity search - Domain/homology
Omega-conotoxin TxVII
Similarity search - Component
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsKobayashi, K. / Sasaki, T. / Sato, K. / Kohno, T.
CitationJournal: Biochemistry / Year: 2000
Title: Three-dimensional solution structure of omega-conotoxin TxVII, an L-type calcium channel blocker.
Authors: Kobayashi, K. / Sasaki, T. / Sato, K. / Kohno, T.
History
DepositionJun 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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: OMEGA-CONOTOXIN TXVII


Theoretical massNumber of molelcules
Total (without water)2,8411
Polymers2,8411
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 / 100structures with the lowest energy
Representative

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Components

#1: Protein/peptide OMEGA-CONOTOXIN TXVII


Mass: 2841.350 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide naturally occurs in Conus textile.
References: UniProt: P56714
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
1422D NOESY
152DQF-COSY
162PE-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
15mM omega-conotoxin TxVII90% H2O/10% D2O
25mM omega-conotoxin TxVIID2O
Sample conditionsIonic strength: 0 / pH: 5.6 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR970101.2Brukercollection
UXNMR970101.2Brukerprocessing
UXNMR970101.2Brukerdata analysis
X-PLOR3.1Brungerdata analysis
X-PLOR3.1Brungerrefinement
X-PLOR3.1Brungerstructure solution
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 452 restraints, 411 are NOE-derived distance constraints, 20 dihedral angle restraints, 21 distance restraints from hydrogen bonds and disulfide bonds.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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