+Open data
-Basic information
Entry | Database: PDB / ID: 2kht | ||||||
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Title | NMR Structure of human alpha defensin HNP-1 | ||||||
Components | Neutrophil defensin 1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / microcrystalline protein / human alpha defensin / Defensin / Secreted / Antibiotic / Antiviral defense / Fungicide / Phosphoprotein | ||||||
Function / homology | Function and homology information pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / collagen-containing extracellular matrix / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLID-STATE NMR / DGSA-distance geometry simulated annealing, simulated annealing | ||||||
Model details | minimized average, model 1 | ||||||
Authors | Zhang, Y. / Li, S. / Doherty, T.F. / Lubkowski, J. / Lu, W. / Li, J. / Barinka, C. / Hong, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR. Authors: Zhang, Y. / Doherty, T. / Li, J. / Lu, W. / Barinka, C. / Lubkowski, J. / Hong, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kht.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kht.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 2kht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/2kht ftp://data.pdbj.org/pub/pdb/validation_reports/kh/2kht | HTTPS FTP |
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-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: 3452.111 Da / Num. of mol.: 1 / Fragment: Residues 65-94 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DEF1, DEFA1, DEFA2, MRS / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P59665 |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR Details: HNP-1 structure determination through 2D & 3D CC and NC correlation experiments by solid state NMR. | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: Polycrystalline sample grown from 60% w/v PEG400, 30 mM Cacodylate, 60 mM Lithium Sulfate | ||||||||||||
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, 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: 28 / Protein psi angle constraints total count: 28 | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average | ||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 12.41 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.53 Å / Maximum torsion angle constraint violation: 22.622 ° / Maximum upper distance constraint violation: 2.68 Å / Torsion angle constraint violation method: TALOS | ||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.58 Å |