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- PDB-8utx: Solution structure of a 12-mer peptide bearing a bicyclic Asx mot... -

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Basic information

Entry
Database: PDB / ID: 8utx
TitleSolution structure of a 12-mer peptide bearing a bicyclic Asx motif mimic (BAMM) as a synthetic N-cap
ComponentsTRP-CYS-ASP-ALA-ALA-CYS-CYS-ALA-ALA-ALA-LYS-ALA-NH2 peptide
KeywordsPEPTIDE BINDING PROTEIN / helix / synthetic N-cap
Function / homology1,3,5-tris(bromomethyl)benzene
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsMi, T.X. / Burgess, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01EY029645 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 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRP-CYS-ASP-ALA-ALA-CYS-CYS-ALA-ALA-ALA-LYS-ALA-NH2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5392
Polymers1,1821
Non-polymers3571
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)50 / 5888structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 1182.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ZBR / 1,3,5-tris(bromomethyl)benzene


Mass: 356.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9Br3
Has ligand of interestN

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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 ROESY

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Sample preparation

DetailsType: solution / Contents: 5 mM Ncap-12-mer, trifluoroethanol/water / Label: peptide / Solvent system: trifluoroethanol/water
SampleConc.: 5 mM / Component: Ncap-12-mer / Isotopic labeling: natural abundance
Sample conditionsIonic strength: water/TFE Not defined / Label: peptide / pH: 5 / Pressure: 1 bar / Temperature: 306 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospinpeak picking
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: 5888 / Conformers submitted total number: 50

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