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- PDB-5xrx: EFK17DA structure in Microgel MAA60 -

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Basic information

Entry
Database: PDB / ID: 5xrx
TitleEFK17DA structure in Microgel MAA60
ComponentsCathelicidin antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / helical and coiled structure / peptide derived from human LL37 / D amino acid isomer
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 / distance geometry
AuthorsDatta, A. / Bhunia, A.
CitationJournal: ACS Appl Mater Interfaces / Year: 2017
Title: Conformational Aspects of High Content Packing of Antimicrobial Peptides in Polymer Microgels
Authors: Singh, S. / Datta, A. / Borro, B.C. / Davoudi, M. / Schmidtchen, A. / Bhunia, A. / Malmsten, M.
History
DepositionJun 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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_software.name
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: Cathelicidin antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)2,1801
Polymers2,1801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2020 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cathelicidin antimicrobial peptide / 18 kDa cationic antimicrobial protein / hCAP-18


Mass: 2179.630 Da / Num. of mol.: 1 / Fragment: UNP residues 149-165 / Source method: obtained synthetically / Details: It is a synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H trNOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM EFK17DA, 55.5 M H2O, 50 M D2O, 25 uM Microgel MAA60, 0.8 mM TSP, 90% H2O/10% D2O
Label: EFK17DA in Maa60 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMEFK17DAnatural abundance1
55.5 MH2Onatural abundance1
50 MD2Onatural abundance1
25 uMMicrogel MAA60natural abundance1
0.8 mMTSPnatural abundance1
Sample conditionsIonic strength: 0.0 mM / Label: condition_1 / pH: 4.5 / PH err: 0.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Ascend TM / Manufacturer: Bruker / Model: Ascend TM / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky3.114Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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