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- PDB-1qfa: STRUCTURE OF A NEUROPEPTIDE Y Y2 AGONIST -

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Basic information

Entry
Database: PDB / ID: 1qfa
TitleSTRUCTURE OF A NEUROPEPTIDE Y Y2 AGONIST
ComponentsPROTEIN (NEUROPEPTIDE Y)
KeywordsHORMONE/GROWTH FACTOR / NEUROPEPTIDE Y / AGONIST / HELIX / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


synaptic signaling via neuropeptide / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / positive regulation of appetite / adult feeding behavior / neuropeptide hormone activity / feeding behavior / neuronal dense core vesicle / central nervous system neuron development / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger ...synaptic signaling via neuropeptide / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / positive regulation of appetite / adult feeding behavior / neuropeptide hormone activity / feeding behavior / neuronal dense core vesicle / central nervous system neuron development / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuropeptide signaling pathway / calcium channel regulator activity / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / GABA-ergic synapse / Peptide ligand-binding receptors / G protein-coupled receptor activity / cerebral cortex development / regulation of blood pressure / neuron projection development / G alpha (i) signalling events / chemical synaptic transmission / signaling receptor binding / Golgi apparatus / 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 / distance geometry
AuthorsBarnham, K.J. / Catalfamo, F. / Pallaghy, P.K. / Howlett, G.J. / Norton, R.S.
CitationJournal: Biochim.Biophys.Acta / Year: 1999
Title: Helical structure and self-association in a 13 residue neuropeptide Y Y2 receptor agonist: relationship to biological activity.
Authors: Barnham, K.J. / Catalfamo, F. / Pallaghy, P.K. / Howlett, G.J. / Norton, R.S.
History
DepositionApr 8, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (NEUROPEPTIDE Y)


Theoretical massNumber of molelcules
Total (without water)1,7741
Polymers1,7741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000LOWEST STEREOCHEMICAL AND NOE ENERGIES
RepresentativeModel #1

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Components

#1: Protein/peptide PROTEIN (NEUROPEPTIDE Y)


Mass: 1774.103 Da / Num. of mol.: 1 / Fragment: NPY Y2 RECEPTOR AGONIST / Mutation: I28L, I31L / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: UniProt: P01303
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY

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Sample preparation

DetailsContents: 40% TFE-D3,60% WATER
Sample conditionspH: 3.6 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
DYANAstructure solution
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST STEREOCHEMICAL AND NOE ENERGIES
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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