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- PDB-1kcn: Structure of e109 Zeta Peptide, an Antagonist of the High-Affinit... -

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Entry
Database: PDB / ID: 1kcn
TitleStructure of e109 Zeta Peptide, an Antagonist of the High-Affinity IgE Receptor
Componentse109 zeta peptide
KeywordsPROTEIN BINDING / disulfide-bonded / helical / "zeta" structure
MethodSOLUTION NMR / hybrid distance geometry, simulated annealing, then further refined by restrained molecular dynamics
AuthorsNakamura, G.R. / Reynolds, M.E. / Chen, Y.M. / Starovasnik, M.A. / Lowman, H.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Stable "zeta" peptides that act as potent antagonists of the high-affinity IgE receptor.
Authors: Nakamura, G.R. / Reynolds, M.E. / Chen, Y.M. / Starovasnik, M.A. / Lowman, H.B.
History
DepositionNov 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: e109 zeta peptide


Theoretical massNumber of molelcules
Total (without water)2,1441
Polymers2,1441
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 / 50structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide e109 zeta peptide


Mass: 2143.615 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 'solid-phase peptide synthesis of a novel peptide based on a naive phage-peptide library that was sorted for binding to the high-affinity IGE receptor'
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
1422D COSY-35
1522D NOESY
1612D ROESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. 3JHNHA WERE OBTAINED BY FITTING LORENTZIAN LINES TO THE ANTIPHASE DOUBLETS OF HN-HA PEAKS IN A 2QF-COSY SPECTRUM ...Text: This structure was determined using standard 2D homonuclear techniques. 3JHNHA WERE OBTAINED BY FITTING LORENTZIAN LINES TO THE ANTIPHASE DOUBLETS OF HN-HA PEAKS IN A 2QF-COSY SPECTRUM PROCESSED TO HIGH DIGITAL RESOLUTION IN F2. 3JHAHB WERE EXTRACTED FROM A COSY-35 SPECTRUM ACQUIRED IN D2O

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM e109 peptide, 92% H2O/8% D2O, pH 5.4, 0.1 mM NaN3, 0.1 mM DSS92% H2O/8% D2O
22mM e109 peptide, 100% D2O, pH 5.4, 0.1 mM NaN3, 0.1 mM DSS100% D2O
Sample conditionspH: 5.4 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker, Inc.collection
Felix98Molecular Simulations, Inc.data analysis
DGII98Molecular Simulations, Inc.structure solution
Discover98Molecular Simulations, Inc.refinement
RefinementMethod: hybrid distance geometry, simulated annealing, then further refined by restrained molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 101 NOE-derived distance restraints, 18 dihedral angle restraints, and 12 distant restraints from 6 hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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