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- PDB-2n09: NMR structure of a short hydrophobic 11mer peptide in DMSO-d6/H2O... -

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Entry
Database: PDB / ID: 2n09
TitleNMR structure of a short hydrophobic 11mer peptide in DMSO-d6/H2O (1:3) solution
ComponentsShort hydrophobic peptide with cyclic constraints
KeywordsDE NOVO PROTEIN / hydrophobic peptide / GLP-1R agonist
MethodSOLUTION NMR / simulated annealing
AuthorsHoang, H.N. / Song, K. / Hill, T.A. / Derksen, D.R. / Edmonds, D.J. / Kok, W.M. / Limberakis, C. / Liras, S. / Loria, P.M. / Mascitti, V. ...Hoang, H.N. / Song, K. / Hill, T.A. / Derksen, D.R. / Edmonds, D.J. / Kok, W.M. / Limberakis, C. / Liras, S. / Loria, P.M. / Mascitti, V. / Mathiowetz, A.M. / Mitchell, J.M. / Piotrowski, D.W. / Price, D.A. / Stanton, R.V. / Suen, J.Y. / Withka, J.M. / Griffith, D.A. / Fairlie, D.P.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Short Hydrophobic Peptides with Cyclic Constraints Are Potent Glucagon-like Peptide-1 Receptor (GLP-1R) Agonists.
Authors: Hoang, H.N. / Song, K. / Hill, T.A. / Derksen, D.R. / Edmonds, D.J. / Kok, W.M. / Limberakis, C. / Liras, S. / Loria, P.M. / Mascitti, V. / Mathiowetz, A.M. / Mitchell, J.M. / Piotrowski, D. ...Authors: Hoang, H.N. / Song, K. / Hill, T.A. / Derksen, D.R. / Edmonds, D.J. / Kok, W.M. / Limberakis, C. / Liras, S. / Loria, P.M. / Mascitti, V. / Mathiowetz, A.M. / Mitchell, J.M. / Piotrowski, D.W. / Price, D.A. / Stanton, R.V. / Suen, J.Y. / Withka, J.M. / Griffith, D.A. / Fairlie, D.P.
History
DepositionMar 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references

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Assembly

Deposited unit
A: Short hydrophobic peptide with cyclic constraints


Theoretical massNumber of molelcules
Total (without water)1,2711
Polymers1,2711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Short hydrophobic peptide with cyclic constraints


Mass: 1271.335 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

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Sample preparation

DetailsContents: 1 mM peptide, 25% DMSO-d6, 75% H2O / Solvent system: 25% DMSO-d6/75% H2O
SampleConc.: 1 mM / Component: peptide-1
Sample conditionsIonic strength: 0.01 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
xplorBrunger, A.T. et al.structure solution
xplorBrunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 96 / NOE intraresidue total count: 30 / NOE medium range total count: 60
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.2 Å

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