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- PDB-6kbo: Three-dimensional LPS bound structure of VG16KRKP-KYE28. -

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Basic information

Entry
Database: PDB / ID: 6kbo
TitleThree-dimensional LPS bound structure of VG16KRKP-KYE28.
Components
  • Heparin cofactor 2
  • VG16KRKP
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Peptide / Nuclear Magnetic Spectroscopy / Peptide Synergism / Lipopolysaccharide (LPS) / Bacterial Membrane
Function / homology
Function and homology information


endopeptidase inhibitor activity / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / chemotaxis / blood coagulation / heparin binding / endoplasmic reticulum lumen ...endopeptidase inhibitor activity / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / chemotaxis / blood coagulation / heparin binding / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Heparin cofactor II, serpin domain / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Biological speciesDengue virus
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsIlyas, H. / Bhunia, A.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insights into the combinatorial effects of antimicrobial peptides reveal a role of aromatic-aromatic interactions in antibacterial synergism.
Authors: Ilyas, H. / Kim, J. / Lee, D. / Malmsten, M. / Bhunia, A.
History
DepositionJun 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VG16KRKP
B: Heparin cofactor 2


Theoretical massNumber of molelcules
Total (without water)5,3692
Polymers5,3692
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area860 Å2
ΔGint-8 kcal/mol
Surface area3990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide VG16KRKP


Mass: 1765.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Dengue virus
#2: Protein/peptide Heparin cofactor 2 / KYE28


Mass: 3604.239 Da / Num. of mol.: 1 / Fragment: Helix-D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05546

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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 NOESY

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Sample preparation

DetailsType: solution
Contents: 0.3 mM 1H, Natural Abundance VG16KRKP, 0.3 mM 1H, Natural Abundance KYE28, 55.55 M 1H, Natural Abundance Water, 10 uM 1H, Natural Abundance Lipopolysaccharide, 90% H2O/10% D2O
Label: VG16KRKP-KYE28 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMVG16KRKP1H, Natural Abundance1
0.3 mMKYE281H, Natural Abundance1
55.55 MWater1H, Natural Abundance1
10 uMLipopolysaccharide1H, Natural Abundance1
Sample conditionsIonic strength: 0.6 mM / Ionic strength err: 0.01 / Label: experiment / pH: 4.5 / PH err: 0.02 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.01

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz
Details: equipped with 5 mm cryogenic cooled triple resonance probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.6Bruker Biospinprocessing
Sparky3.113Goddardchemical shift assignment
CYANAv2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANAv2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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