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- PDB-1haj: A beta-Hairpin Structure in a 13-mer Peptide that Binds a-Bungaro... -

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Basic information

Entry
Database: PDB / ID: 1haj
TitleA beta-Hairpin Structure in a 13-mer Peptide that Binds a-Bungarotoxin with High Affinity and Neutralizes its Toxicity
Components
  • ALPHA-BUNGAROTOXIN
  • PEPTIDE
KeywordsTOXIN/PEPTIDE / COMPLEX (TOXIN-PEPTIDE) / ACETYLCHOLINE RECEPTOR MIMITOPE / ALPHA-BUNGAROTOXIN / PROTEIN-PEPTIDE COMPLEX / TOXIN / BETA-HAIRPIN / TOXIN-PEPTIDE complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin/toxin-like / Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily ...Snake toxin/toxin-like / Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Alpha-bungarotoxin / Alpha-bungarotoxin
Similarity search - Component
Biological speciesBUNGARUS MULTICINCTUS (many-banded krait)
SYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING
AuthorsScherf, T. / Kasher, R. / Balass, M. / Fridkin, M. / Fuchs, S. / Katchalski-Katzir, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A Beta-Hairpin Structure in a 13-mer Peptide that Binds Alpha-Bungarotoxin with High Affinity and Neutralizes its Toxicity
Authors: Scherf, T. / Kasher, R. / Balass, M. / Fridkin, M. / Fuchs, S. / Katchalski-Katzir, E.
#1: Journal: Chem.Biol. / Year: 2001
Title: Design and Synthesis of Peptides that Bind A-Bungarotoxin with High Affinity
Authors: Kasher, R. / Balass, M. / Scherf, T. / Fridkin, M. / Fuchs, S. / Katchalski-Katzir, E.
History
DepositionApr 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name
Remark 700 SHEET DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM STRAND: S1A 1; STRANDS S2D & S2E FORM B- ... SHEET DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM STRAND: S1A 1; STRANDS S2D & S2E FORM B-HAIRPIN WITHIN THE BOUND PEPTIDE, THAT COMBINES TO S2A-S2C TO FORM 5-STRANDED INTERMOLECULAR BETA-SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-BUNGAROTOXIN
B: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)9,7112
Polymers9,7112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-8 kcal/mol
Surface area5530 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -NO RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein ALPHA-BUNGAROTOXIN / LONG NEUROTOXIN 1 / BGTX / ALPHA-BTX / A-BTX


Mass: 8005.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ALPHA-NEUROTOXIN / Source: (natural) BUNGARUS MULTICINCTUS (many-banded krait) / Secretion: VENOM / References: UniProt: P01378, UniProt: P60615*PLUS
#2: Protein/peptide PEPTIDE / HIGH AFFINITY PEPTIDE


Mass: 1705.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MIMOTOPE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR / Source: (synth.) SYNTHETIC CONSTRUCT (others)
Compound detailsTHE PEPTIDE BINDS ALPHA-BUNGAROTOXIN AND THUS INHIBITS THE BINDING OF THE TOXIN TO THE NICOTINIC ...THE PEPTIDE BINDS ALPHA-BUNGAROTOXIN AND THUS INHIBITS THE BINDING OF THE TOXIN TO THE NICOTINIC RECEPTORS. THE OBSERVED QUATERNARY STATE IS MONOMERIC IN SOLUTION WHILE IN THE CRYSTAL STRUCTURES IT IS OBSERVED TO BE DIMERIC
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121HOHAHA
131DQF-COSY
NMR detailsText: THE STRUCTURES WERE DETERMINED USING STANDARD 2D 1H-NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 1MM COMPLEX IN 90% WATER,10% D2O
Sample conditionspH: 6 / Pressure: AMBIENT / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.9BRUNGER, ADAMS, CLORE, DELANO, GROS ET ALrefinement
XwinNMRstructure solution
AURELIAstructure solution
CNSstructure solution
RefinementMethod: DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: RMS DEVIATIONS FROM IDEAL VALUES: BOND LENGTH (A) 0.0033,ANGLES (DEG) 0.52 IMPROPERS (DEG) 0.45
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATION / Conformers submitted total number: 10

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