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- PDB-2k6o: Human LL-37 Structure -

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Basic information

Entry
Database: PDB / ID: 2k6o
TitleHuman LL-37 Structure
ComponentsCathelicidin antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / Human host defense peptide / Human cathelicidin / antimicrobial peptide / LL-37 / Bacterial membrane targeting / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Pyrrolidone carboxylic acid / Secreted
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 detailsNMR Structure of human cathelicidin LL-37 in complex with detergent micelles
AuthorsWang, G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles
Authors: Wang, G.
History
DepositionJul 14, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathelicidin antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)4,5041
Polymers4,5041
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)4 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Cathelicidin antimicrobial peptide / 18 kDa cationic antimicrobial protein / CAP-18 / hCAP-18 / Antibacterial protein FALL-39 / FALL-39 ...18 kDa cationic antimicrobial protein / CAP-18 / hCAP-18 / Antibacterial protein FALL-39 / FALL-39 peptide antibiotic / Antibacterial protein LL-37


Mass: 4504.351 Da / Num. of mol.: 1 / Fragment: residues 134-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMP, CAP18, FALL39, HSD26 / Plasmid details: pET-32a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P49913

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR Structure of human cathelicidin LL-37 in complex with detergent micelles
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HBHA(CO)NH
1513D HN(CO)CA
1613D H(CCO)NH
1713D HNCO
1813D C(CO)NH
1913D (H)CCH-TOCSY
11013D HNHA

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Sample preparation

DetailsContents: 0.50 mM [U-100% 15N] LL-37, 0.5 mM [U-100% 13C; U-100% 15N] LL-37, 2 mM LL-37, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.50 mM / Component: LL-37 / Isotopic labeling: [U-100% 15N; U-100% 13C]
Sample conditionsIonic strength: non-buffered / pH: 5.4 / Pressure: ambient atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloredata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 345 / NOE intraresidue total count: 124 / NOE long range total count: 0 / NOE medium range total count: 94 / NOE sequential total count: 128 / Protein phi angle constraints total count: 29 / Protein psi angle constraints total count: 29
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 4

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