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- PDB-1d6b: SOLUTION STRUCTURE OF DEFENSIN-LIKE PEPTIDE-2 (DLP-2) FROM PLATYP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d6b | ||||||
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Title | SOLUTION STRUCTURE OF DEFENSIN-LIKE PEPTIDE-2 (DLP-2) FROM PLATYPUS VENOM | ||||||
![]() | DEFENSIN-LIKE PEPTIDE-2 | ||||||
![]() | TOXIN / HELIX / ANTIPARALLEL BETA-SHEET | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS, TORSION ANGLE DYNAMICS | ||||||
![]() | Torres, A.M. / De Plater, G.M. / Doverskog, M. / C Birinyi-Strachan, L. / Nicholson, G.M. / Gallagher, C.H. / Kuchel, P.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.1 KB | Display | ![]() |
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PDB format | ![]() | 228.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 342.3 KB | Display | ![]() |
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Full document | ![]() | 519.6 KB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 5121.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: THE STRUCTURES WERE DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. |
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Sample preparation
Details | Contents: 1MM DLP-2 |
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Sample conditions | Ionic strength: NO SALT ADDED / pH: 3.6 / Pressure: AMBIENT / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 4800 / Conformers submitted total number: 20 |