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Yorodumi- PDB-5xbd: Disulfide-constrained Wound Healing Peptide Derived from Pereskia bleo -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xbd | |||||||||
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Title | Disulfide-constrained Wound Healing Peptide Derived from Pereskia bleo | |||||||||
Components | pB1 | |||||||||
Keywords | UNKNOWN FUNCTION / Disulfide bond / Pereskia bleo / Cystein-rich peptide CRP / anti-microbial peptide | |||||||||
Function / homology | Gurmarin/antifungal peptide / pB1 Function and homology information | |||||||||
Biological species | Pereskia bleo (plant) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Xiao, T. / Tam, J.P. | |||||||||
Citation | Journal: Front Plant Sci / Year: 2017 Title: Bleogens: Cactus-Derived Anti-Candida Cysteine-Rich Peptides with Three Different Precursor Arrangements Authors: Loo, S. / Kam, A. / Xiao, T. / Tam, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xbd.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xbd.ent.gz | 170.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xbd_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 5xbd_full_validation.pdf.gz | 645.4 KB | Display | |
Data in XML | 5xbd_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 5xbd_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/5xbd ftp://data.pdbj.org/pub/pdb/validation_reports/xb/5xbd | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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: 3838.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pereskia bleo (plant) / References: UniProt: A0A2R2JFU8*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1.5 mM pB1, 55.56 M H2O, 2.92 M [U-100% 2H] D2O, 0.03 % TFA, 95% H2O/5% D2O Label: pB1 / Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 mM / Label: condition_1 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |