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- PDB-2ncw: NMR structure of WWWKYE21 structure in LPS micelles -

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Basic information

Entry
Database: PDB / ID: 2ncw
TitleNMR structure of WWWKYE21 structure in LPS micelles
ComponentsHeparin cofactor 2
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsDatta, A. / Bhunia, A.
CitationJournal: Sci Rep / Year: 2017
Title: Tryptophan end-tagging for promoted lipopolysaccharide interactions and anti-inflammatory effects.
Authors: Singh, S. / Datta, A. / Schmidtchen, A. / Bhunia, A. / Malmsten, M.
History
DepositionApr 18, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Nov 3, 2021Group: Data collection / Database references / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.model / _pdbx_nmr_spectrometer.type / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: Heparin cofactor 2


Theoretical massNumber of molelcules
Total (without water)3,3101
Polymers3,3101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 Heparin cofactor 2 / Heparin cofactor II / HC-II / Protease inhibitor leuserpin-2 / HLS2 / Serpin D1


Mass: 3309.912 Da / Num. of mol.: 1 / Fragment: Glycosaminoglycan-binding site residues 189-212 / Mutation: L192R, Y193W, E194S / 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-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM protein, 1 mM DSS, 10 mM sodium phosphate, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMproteinnatural abundance1
1 mMDSSnatural abundance1
10 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 0.01 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1
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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