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- PDB-1d6b: SOLUTION STRUCTURE OF DEFENSIN-LIKE PEPTIDE-2 (DLP-2) FROM PLATYP... -

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Basic information

Entry
Database: PDB / ID: 1d6b
TitleSOLUTION STRUCTURE OF DEFENSIN-LIKE PEPTIDE-2 (DLP-2) FROM PLATYPUS VENOM
ComponentsDEFENSIN-LIKE PEPTIDE-2
KeywordsTOXIN / HELIX / ANTIPARALLEL BETA-SHEET
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Defensin-like peptide / Defensin-like peptide family / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Defensin-like peptide 2/4
Similarity search - Component
Biological speciesOrnithorhynchus anatinus (platypus)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS, TORSION ANGLE DYNAMICS
AuthorsTorres, A.M. / De Plater, G.M. / Doverskog, M. / C Birinyi-Strachan, L. / Nicholson, G.M. / Gallagher, C.H. / Kuchel, P.W.
Citation
Journal: Biochem.J. / Year: 2000
Title: Defensin-like peptide-2 from platypus venom: member of a class of peptides with a distinct structural fold.
Authors: Torres, A.M. / de Plater, G.M. / Doverskog, M. / Birinyi-Strachan, L.C. / Nicholson, G.M. / Gallagher, C.H. / Kuchel, P.W.
#1: Journal: Biochem.J. / Year: 1999
Title: Solution Structure of a Defensin-Like Peptide From Platypus Venom
Authors: Torres, A.M. / Wang, X. / Fletcher, J.I. / Alewood, D. / Alewood, P.F. / Smith, R. / Simpson, R.J. / Nicholson, G.M. / Sutherland, S.K. / Gallagher, C.H. / King, G.F. / Kuchel, P.W.
#2: Journal: Biochemistry / Year: 1995
Title: Solution Structure of Bovine Neutrophil Beta-Defensin-12: The Peptide Fold of the Beta-Defensins is Identical to That of the Classical Defensins
Authors: Zimmermann, G.R. / Legault, P. / Selsted, M.E. / Pardi, A.
History
DepositionOct 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 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: 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
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
Revision 1.4Oct 30, 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: DEFENSIN-LIKE PEPTIDE-2


Theoretical massNumber of molelcules
Total (without water)5,1221
Polymers5,1221
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 / 4800LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide DEFENSIN-LIKE PEPTIDE-2


Mass: 5121.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ornithorhynchus anatinus (platypus) / Organ: SPUR / Secretion: VENOM / Tissue: VENOM GLAND / References: UniProt: P82140
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: THE STRUCTURES WERE DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 1MM DLP-2
Sample conditionsIonic strength: NO SALT ADDED / pH: 3.6 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5BRUKERprocessing
XEASY1.3.13BARTELS, C., XIA, T., BILLETER, M., GUNTERT, P., WUTHRICH, K.data analysis
DYANA1.5GUNTERT, P., MUMENTHALER, C., WUHTRICH, K.structure solution
X-PLOR3.843BRUNGERrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS, TORSION ANGLE DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 739 RESTRAINTS, 699 ARE NOE-DERIVED DISTANCE RESTRAINTS, 24 DIHEDRAL ANGLE RESTRAINTS, 16 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 4800 / Conformers submitted total number: 20

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