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- PDB-1fh3: NMR STRUCTURES OF LQH III ALPHA-LIKE SCORPION TOXIN FROM LEIURUS ... -

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Basic information

Entry
Database: PDB / ID: 1fh3
TitleNMR STRUCTURES OF LQH III ALPHA-LIKE SCORPION TOXIN FROM LEIURUS QUINQUESTRIATUS CORRESPONDING TO THE MAJOR CONFORMER IN SOLUTION
ComponentsLQH III ALPHA-LIKE TOXIN
KeywordsTOXIN / ALPHA-LIKE TOXIN / SCORPION TOXIN / SODIUM CHANNEL INHIBITOR NON-PROLINE CIS PEPTIDE BOND / CIS-TRANS ISOMERISM
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-like toxin Lqh3
Similarity search - Component
Biological speciesLeiurus quinquestriatus hebraeus (scorpion)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsKrimm, I. / Trivelli, X. / Lancelin, J.M.
Citation
Journal: To be Published
Title: A Cis-trans Isomerism of a Non-prolyl Peptide Bond in Lqh III Alpha-like Scorpion Toxin Revealed by Solution NMR
Authors: Krimm, I. / Trivelli, X. / Lancelin, J.M.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: NMR Structures and Activity of a Novel Alpha-like Toxin from the Scorpion Leiurus Quinquestriatus hebraeus
Authors: Krimm, I. / Gilles, N. / Sautiere, P. / Stankiewicz, M. / Pelhate, M. / Gordon, D. / Lancelin, J.M.
History
DepositionJul 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: LQH III ALPHA-LIKE TOXIN


Theoretical massNumber of molelcules
Total (without water)7,0641
Polymers7,0641
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)42 / 80structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #25closest to the average

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Components

#1: Protein LQH III ALPHA-LIKE TOXIN


Mass: 7063.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: AMIDATED AT THE C-TERMINAL POSITION(CONH2). THIS STRUCTURE IS IN EQUILIBRIUM WITH THE PRO9-GLU10 TRANS ISOMER (1BMR).
Source: (natural) Leiurus quinquestriatus hebraeus (scorpion)
Secretion: VENOM / Species: Leiurus quinquestriatus / Strain: hebraeus / References: UniProt: P56678
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

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Sample preparation

DetailsContents: 2mM LqhIII; 100 mM phosphate buffer pH 5.8; 90% H2O 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: NA / pH: 5.8 / Pressure: 1 atm / Temperature: 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.2Delsucdata analysis
XwinNMRNABrukercollection
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 42

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