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- PDB-2nou: Membrane induced structure of Scyliorhinin I: A Dual NK1/NK2 agonist -

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Basic information

Entry
Database: PDB / ID: 2nou
TitleMembrane induced structure of Scyliorhinin I: A Dual NK1/NK2 agonist
ComponentsScyliorhinin I
KeywordsNEUROPEPTIDE / Helix / 3-10 Helix / Lipid induced Conformation / DPC micelles
Function / homologyTachykinin/Neurokinin-like, conserved site / Tachykinin family signature. / neuropeptide signaling pathway / extracellular region / Scyliorhinin-1
Function and homology information
MethodSOLUTION NMR / Distance geometry, simulated annealing (DYANA)
AuthorsDike, A. / Cowsik, S.M.
CitationJournal: Biophys.J. / Year: 2005
Title: Membrane induced structure of Scyliorhinin I: A Dual NK1/NK2 agonist
Authors: Dike, A. / Cowsik, S.M.
History
DepositionOct 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scyliorhinin I


Theoretical massNumber of molelcules
Total (without water)1,2211
Polymers1,2211
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 the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Scyliorhinin I


Mass: 1221.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was Chemically Synthesized / References: UniProt: P08608

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 5 mM Scyliorhinin I, 200 mM perdeuterated DPC, 90%H2O, 10%D2O, pH 4.5
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.5 / Pressure: 1 atm / Temperature: 315 K

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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
DYANA1.5Guntert, P. et al.structure solution
XwinNMR3.1BRUKERprocessing
DYANA1.5Guntert, P. et al.refinement
RefinementMethod: Distance geometry, simulated annealing (DYANA) / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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