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- PDB-2dez: Structure of human PYY -

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Basic information

Entry
Database: PDB / ID: 2dez
TitleStructure of human PYY
ComponentsPeptide YY
KeywordsNEUROPEPTIDE / PP-fold / helix
Function / homology
Function and homology information


neuropeptide Y receptor binding / intestinal epithelial cell differentiation / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor binding / hormone activity / G alpha (i) signalling events / extracellular space / extracellular region
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
MethodSOLUTION NMR / simulated annealing
AuthorsNygaard, R.
CitationJournal: Biochemistry / Year: 2006
Title: The PP-Fold Solution Structure of Human Polypeptide YY and Human PYY3-36 As Determined by NMR(,)
Authors: Nygaard, R. / Nielbo, S. / Schwartz, T.W. / Poulsen, F.M.
History
DepositionFeb 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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 / _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 20, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide YY


Theoretical massNumber of molelcules
Total (without water)4,3151
Polymers4,3151
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptide YY / polypeptide YY / PYY / PYY-I / Peptide tyrosine tyrosine


Mass: 4314.795 Da / Num. of mol.: 1 / Fragment: Peptide YY / Source method: obtained synthetically
Details: This sequence occurs naturally in humans.; This protein synthesized by solid state peptide synthesis.
References: UniProt: P10082
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D TOCSY
1312D NOESY

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Sample preparation

DetailsContents: 1mM human PYY; pH 4.6 by addition of NaOH and HCl; 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionspH: 4.6 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, F.processing
Pronto3DKjaer, M.data analysis
CYANA1Guntert, P.structure solution
XPLOR-NIH2.9Schwieters, C.structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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