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- PDB-1icy: [ALA31,PRO32]-PNPY BOUND TO DPC MICELLES -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1icy
Title[ALA31,PRO32]-PNPY BOUND TO DPC MICELLES
ComponentsNEUROPEPTIDE Y
KeywordsHORMONE/GROWTH FACTOR / Y5 Receptor selective NPY mutant / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


neuropeptide Y receptor binding / positive regulation of appetite / adult feeding behavior / neuropeptide hormone activity / feeding behavior / neuronal dense core vesicle / neuropeptide signaling pathway / extracellular space
Similarity search - Function
Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBader, R. / Rytz, G. / Lerch, M. / Beck-Sickinger, A.G. / Zerbe, O.
CitationJournal: Biochemistry / Year: 2002
Title: Key motif to gain selectivity at the neuropeptide Y5-receptor: structure and dynamics of micelle-bound [Ala31, Pro32]-NPY.
Authors: Bader, R. / Rytz, G. / Lerch, M. / Beck-Sickinger, A.G. / Zerbe, O.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROPEPTIDE Y


Theoretical massNumber of molelcules
Total (without water)4,2131
Polymers4,2131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 100structures with NMR energies less than 3 kcal/mol
Representative

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Components

#1: Protein/peptide NEUROPEPTIDE Y / / NPY


Mass: 4212.621 Da / Num. of mol.: 1 / Mutation: I31A, T32P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: PUBK19-APNPY-G / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01304

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM 31Ala,32Pro NPY, 300mM DPC, pH=6.0 90%H2O, 10% D2O90% H2O/10% D2O
22 mM 31Ala,32Pro NPY, 300mM DPC, pH=6.0 99.9%D2O99.9%D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 6.0 1 atm310 K
20 6.0 1 atm310 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukerprocessing
XEASY1.53Bartels et aldata analysis
DYANA1.5Guentert et alstructure solution
OPAL (AMBER)1.6Lunginbuehl et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 622 NOE cross peaks and 16 HNHA couplings indicative of non-averaged backbone conformations
NMR ensembleConformer selection criteria: structures with NMR energies less than 3 kcal/mol
Conformers calculated total number: 100 / Conformers submitted total number: 17

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