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- PDB-9d9c: Incorporation of dehydro-aza-proline residues in avian pancreatic... -

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Basic information

Entry
Database: PDB / ID: 9d9c
TitleIncorporation of dehydro-aza-proline residues in avian pancreatic polypeptide: Aza-Pro substitution at positions 4 and 6
ComponentsPancreatic polypeptide
KeywordsSIGNALING PROTEIN / PANCREATIC HORMONE / MODIFIED BACKBONE
Function / homology
Function and homology information


neuropeptide Y receptor binding / neuropeptide hormone activity / feeding behavior / 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
Pancreatic polypeptide
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodSOLUTION NMR / simulated annealing
AuthorsWright, M.M. / Rajewski, B.H. / Gerrein, T.A. / Smith, L.J. / Horne, W.S. / Del Valle, J.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE2109008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149220 United States
CitationJournal: Commun Chem / Year: 2025
Title: Stabilization of a miniprotein fold by an unpuckered proline surrogate.
Authors: Wright, M.M. / Rajewski, B.H. / Gerrein, T.A. / Xu, Z. / Smith, L.J. / Seth Horne, W. / Del Valle, J.R.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pancreatic polypeptide
B: Pancreatic polypeptide


Theoretical massNumber of molelcules
Total (without water)8,4072
Polymers8,4072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Pancreatic polypeptide / PP


Mass: 4203.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Meleagris gallopavo (turkey) / References: UniProt: P68249
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 2 mM avian pancreatic polypeptide, dehydro-aza-proline substitution at residues 4 and 6, 50 mM [U-2H] sodium acetate, 0.05 mM DSS, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMavian pancreatic polypeptide, dehydro-aza-proline substitution at residues 4 and 6natural abundance1
50 mMsodium acetate[U-2H]1
0.05 mMDSSnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 4.1 pH* / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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