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- PDB-8un8: Solution conformations of a 12-mer peptide bearing a natural N-hy... -

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Entry
Database: PDB / ID: 8un8
TitleSolution conformations of a 12-mer peptide bearing a natural N-hydrophobic triangle
ComponentsACE-LEU-ASP-ALA-ALA-LEU-LEU-ALA-ALA-ALA-LYS-ALA-TRP-NH2 peptide
KeywordsPROTEIN BINDING / hydrophobic triangle
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsMi, T.X. / Burgess, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01EY029645 United States
National Science Foundation (NSF, United States)CHE 1608009 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21NS130471-01A1 United States
CitationJournal: Nat Commun / Year: 2024
Title: Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs).
Authors: Mi, T. / Nguyen, D. / Gao, Z. / Burgess, K.
History
DepositionOct 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ACE-LEU-ASP-ALA-ALA-LEU-LEU-ALA-ALA-ALA-LYS-ALA-TRP-NH2 peptide


Theoretical massNumber of molelcules
Total (without water)1,2381
Polymers1,2381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 2780structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ACE-LEU-ASP-ALA-ALA-LEU-LEU-ALA-ALA-ALA-LYS-ALA-TRP-NH2 peptide


Mass: 1238.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN
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
111isotropic11D
121isotropic12D COSY
131isotropic12D TOCSY
141isotropic12D NOESY

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Sample preparation

DetailsType: solution / Contents: 4 mM LDLL 12-mer, 75% H2O/5% D2O/20% TFE-D3 / Details: 4 mM peptide 75% H2O 5% D2O 20% TFE-D3 / Label: LDLL 12-mer / Solvent system: 75% H2O/5% D2O/20% TFE-D3
SampleConc.: 4 mM / Component: LDLL 12-mer / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 5 mM peptide Not defined / Label: TFE/H2O / pH: 5 / Pressure: 1 bar / Temperature: 306 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE 500 / Manufacturer: Bruker / Model: AVANCE 500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospinpeak picking
MacroModelSchrodingerrefinement
MacroModelSchrodingerstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2780 / Conformers submitted total number: 23

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