+Open data
-Basic information
Entry | Database: PDB / ID: 1b8w | ||||||
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Title | DEFENSIN-LIKE PEPTIDE 1 | ||||||
Components | PROTEIN (DEFENSIN-LIKE PEPTIDE 1) | ||||||
Keywords | TOXIN / PLATYPUS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ornithorhynchus anatinus (platypus) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING | ||||||
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. ...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. | ||||||
Citation | 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. #1: Journal: Toxicon / Year: 1995 Title: A Pharmacological and Biochemical Investigation of the Venom from the Platypus (Ornithorhynchus anatinus) Authors: De Plater, G. / Martin, R.L. / Milburn, P.J. #2: Journal: To Be Published / Year: 1983 Title: Australian Animal Toxins: The Creatures, Their Toxins and Care of the Poisoned Patient Authors: Sutherland, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b8w.cif.gz | 266.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8w.ent.gz | 220.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b8w_validation.pdf.gz | 340.2 KB | Display | wwPDB validaton report |
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Full document | 1b8w_full_validation.pdf.gz | 506.2 KB | Display | |
Data in XML | 1b8w_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 1b8w_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8w ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8w | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4968.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM PLATYPUS VENOM / Source: (natural) Ornithorhynchus anatinus (platypus) / Organ: SPUR / Secretion: VENOM / Tissue: VENOM GLAND / References: UniProt: P82172 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING 1D AND 2D NMR SPECTROSCOPY USING CHEMICALLY SYNTHESIZED DLP-1. |
-Sample preparation
Details | Contents: 3.4MM |
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Sample conditions | pH: 3.9 / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 Details: REFINEMENT WAS CARRIED-OUT BY SIMULATED ANNEALING PROTOCOL USING SIMPLIFIED ALL-HYDROGEN FORCE FIELD AND STANDARD X-PLOR PARAMATERS FOR COVALENT GEOMETRY. | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 1000 / Conformers submitted total number: 20 |