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- PDB-1q01: Lebetin peptides, a new class of potent aggregation inhibitors -

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Basic information

Entry
Database: PDB / ID: 1q01
TitleLebetin peptides, a new class of potent aggregation inhibitors
Componentslebetin 2 isoform alpha
KeywordsBLOOD CLOTTING / BETA-BULGED HAIRPAIN
Function / homology
Function and homology information


hormone activity / regulation of blood pressure / toxin activity / extracellular region
Similarity search - Function
Natriuretic peptide, brain type / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide
Similarity search - Domain/homology
Biological speciesMacrovipera lebetina (snake)
MethodSOLUTION NMR / Diana, CNS, distance geometry, simulated annealing
AuthorsMosbah, A. / Marrakchi, N. / Ganzalez, M.J. / Van Rietschoten, J. / Giralt, E. / El Ayeb, M. / Rochat, H. / Sabatier, J.M. / Darbon, H. / Mabrouk, K.
CitationJournal: To be Published
Title: Lebetin peptides, a new class of potent aggregation inhibitors
Authors: Mosbah, A. / Marrakchi, N. / Ganzalez, M.J. / Van Rietschoten, J. / Giralt, E. / El Ayeb, M. / Rochat, H. / Sabatier, J.M. / Darbon, H. / Mabrouk, K.
History
DepositionJul 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lebetin 2 isoform alpha


Theoretical massNumber of molelcules
Total (without water)3,9541
Polymers3,9541
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)24 / 50back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1fewest violations, lowest energy

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Components

#1: Protein/peptide lebetin 2 isoform alpha


Mass: 3954.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macrovipera lebetina (snake) / Secretion: venom / References: UniProt: Q7LZ09

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
241DQF-COSY
2512D TOCSY
2612D NOESY

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Sample preparation

Details
Solution-IDContents
190% H2O, 10% D2O
290% H2O, 10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13 ambient 280 K
23 ambient 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameClassification
XwinNMRcollection
XwinNMRprocessing
XEASYdata analysis
DIANAstructure solution
CNSrefinement
RefinementMethod: Diana, CNS, distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the ...Conformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 50 / Conformers submitted total number: 24

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