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- PDB-2ksg: Solution structure of dermcidin-1L, a human antibiotic peptide -

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Basic information

Entry
Database: PDB / ID: 2ksg
TitleSolution structure of dermcidin-1L, a human antibiotic peptide
ComponentsDermcidin
KeywordsANTIBIOTIC / 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
Helix Hairpins - #580 / Dermcidin / Dermcidin/Lacritin / Dermcidin, antibiotic peptide / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 17
AuthorsJung, H. / Yang, S. / Kim, J.
CitationJournal: To be Published
Title: Solution structure and membrane interactions of dermcidin-1L, a human antibiotic peptide
Authors: Jung, H. / Yang, S. / Kim, J.
History
DepositionJan 4, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dermcidin


Theoretical massNumber of molelcules
Total (without water)4,8271
Polymers4,8271
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Dermcidin / / Preproteolysin / Survival-promoting peptide / DCD-1


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1413D HNHA

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Sample preparation

DetailsContents: 50% [U-99% 2H] TFE-1, 10% [U-99% 2H] D2O-2, 40% H2O-3, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 %TFE-1[U-99% 2H]1
10 %D2O-2[U-99% 2H]1
40 %H2O-31
Sample conditionspH: 4.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsProtein 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 representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 17

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