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Yorodumi- PDB-2mfs: Solution NMR structure of the cactus-derived antimicrobial peptid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mfs | ||||||
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Title | Solution NMR structure of the cactus-derived antimicrobial peptide Ep-AMP1 | ||||||
Components | Ep-AMP1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / cystine-knot | ||||||
Biological species | Synthetic (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Rosengren, K. / Goransson, U. / Gunasekera, S. / Aboye, T.L. | ||||||
Citation | Journal: Chembiochem / Year: 2015 Title: A cactus-derived toxin-like cystine knot Peptide with selective antimicrobial activity. Authors: Aboye, T.L. / Stromstedt, A.A. / Gunasekera, S. / Bruhn, J.G. / El-Seedi, H. / Rosengren, K.J. / Goransson, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mfs.cif.gz | 189 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mfs.ent.gz | 158.9 KB | Display | PDB format |
PDBx/mmJSON format | 2mfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mfs_validation.pdf.gz | 527 KB | Display | wwPDB validaton report |
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Full document | 2mfs_full_validation.pdf.gz | 627.9 KB | Display | |
Data in XML | 2mfs_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2mfs_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/2mfs ftp://data.pdbj.org/pub/pdb/validation_reports/mf/2mfs | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3611.230 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was assembled using standard Fmoc based solid phase peptide synthesis. Source: (synth.) Synthetic (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 298 K |
-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: simulated annealing / Software ordinal: 1 Details: Simulated annealing followed by refinement and energy minimization in explicit solvent. | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 347 / NOE intraresidue total count: 0 / NOE long range total count: 142 / NOE medium range total count: 51 / NOE sequential total count: 154 / Hydrogen bond constraints total count: 30 / Protein chi angle constraints total count: 7 / Protein phi angle constraints total count: 23 / Protein psi angle constraints total count: 22 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |