+Open data
-Basic information
Entry | Database: PDB / ID: 2ksg | ||||||
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Title | Solution structure of dermcidin-1L, a human antibiotic peptide | ||||||
Components | Dermcidin | ||||||
Keywords | ANTIBIOTIC / antibiotic peptide / peptide-membrane interaction / amphipathic alpha helix | ||||||
Function / homology | Function and homology information killing by host of symbiont cells / Hydrolases; Acting on peptide bonds (peptidases) / Antimicrobial peptides / defense response to fungus / monoatomic ion channel activity / peptidase activity / defense response to bacterium / lipid binding / proteolysis / RNA binding ...killing by host of symbiont cells / Hydrolases; Acting on peptide bonds (peptidases) / Antimicrobial peptides / defense response to fungus / monoatomic ion channel activity / peptidase activity / defense response to bacterium / lipid binding / proteolysis / RNA binding / extracellular exosome / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | closest to the average, model 17 | ||||||
Authors | Jung, H. / Yang, S. / Kim, J. | ||||||
Citation | Journal: To be Published Title: Solution structure and membrane interactions of dermcidin-1L, a human antibiotic peptide Authors: Jung, H. / Yang, S. / Kim, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ksg.cif.gz | 309.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ksg.ent.gz | 273 KB | Display | PDB format |
PDBx/mmJSON format | 2ksg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/2ksg ftp://data.pdbj.org/pub/pdb/validation_reports/ks/2ksg | HTTPS FTP |
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-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: 4826.503 Da / Num. of mol.: 1 / Fragment: DCD-1, residues in UNP 63-110 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCD, AIDD, DSEP / Production host: Escherichia coli (E. coli) / References: UniProt: P81605 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 50% [U-99% 2H] TFE-1, 10% [U-99% 2H] D2O-2, 40% H2O-3, trifluoroethanol/water Solvent system: trifluoroethanol/water | ||||||||||||||||
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Sample |
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Sample conditions | pH: 4.2 / 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: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||
NMR constraints | Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 0 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 17 |