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- PDB-2na3: NMR Structure of KR-12: A minimalized domain derived from the hum... -

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Basic information

Entry
Database: PDB / ID: 2na3
TitleNMR Structure of KR-12: A minimalized domain derived from the human cathelicidin LL-37
ComponentsAntibacterial protein LL-37Antibiotic
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / helical / cathelicidin
Function / homology
Function and homology information


cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection ...cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection / lipopolysaccharide binding / specific granule lumen / positive regulation of angiogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / cellular response to tumor necrosis factor / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cystatin superfamily
Similarity search - Domain/homology
Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsGunasekera, S. / Goransson, U.
CitationJournal: To be Published
Title: Backbone-cyclized stable peptide-dimers derived from the human cathelicidin LL-37 mediate potent antimicrobial activity
Authors: Gunasekera, S. / Muhammad, T. / Stromstedt, A.A. / Rosengren, K.J. / Goransson, U.
History
DepositionDec 21, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibacterial protein LL-37


Theoretical massNumber of molelcules
Total (without water)1,5771
Polymers1,5771
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)15 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Antibacterial protein LL-37 / Antibiotic


Mass: 1576.951 Da / Num. of mol.: 1 / Fragment: UNP residues 151-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMP, CAP18, FALL39, HSD26 / References: UniProt: P49913

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY
1412D 1H-15N HSQC
2522D 1H-13C HSQC
2622D 1H-1H TOCSY
2722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
190 % v/v H2O, 10 % v/v D2O, 90% H2O/10% D2O90% H2O/10% D2O
2100 % v/v D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
90 v/vH2O-11
10 v/vD2O-21
100 v/vD2O-32
Sample conditions
Conditions-IDpHTemperature (K)
14.5 298 K
24.5 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CYANA / Version: 3 / Developer: Guntert, P. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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