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- PDB-8qn2: Helical foldamers as selective G-quadruplex ligands -

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Basic information

Entry
Database: PDB / ID: 8qn2
TitleHelical foldamers as selective G-quadruplex ligands
Components
  • ACE-QUK-QUK-ZY9-QUK
  • DNA (5'-D(*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')
KeywordsGENE REGULATION / Complex / Foldamer / G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKoenig, A. / Thore, S. / Gabelica, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE29-0013 POLYnESI France
CitationJournal: To Be Published
Title: Helical foldamers as selective G-quadruplex ligands
Authors: Koenig, A. / Laffile, V. / Largy, E. / Thore, S. / Mackereth, C. / Ferrand, Y. / Gabelica, V.
History
DepositionSep 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 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: DNA (5'-D(*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')
B: ACE-QUK-QUK-ZY9-QUK
C: ACE-QUK-QUK-ZY9-QUK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3218
Polymers8,1553
Non-polymers1665
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.710, 32.710, 61.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z

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Components

#1: DNA chain DNA (5'-D(*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')


Mass: 6339.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) synthetic construct (others)
#2: Protein/peptide ACE-QUK-QUK-ZY9-QUK


Mass: 907.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: potassium chloride, magnesium chloride, PEG 550, Tris (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30.51 Å / Num. obs: 2226 / % possible obs: 99.1 % / Redundancy: 13.4 % / Biso Wilson estimate: 58.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.0426 / Rrim(I) all: 0.1531 / Net I/σ(I): 21.61
Reflection shellResolution: 2.51→2.6 Å / Rmerge(I) obs: 1.054 / Mean I/σ(I) obs: 4.09 / Num. unique obs: 218 / CC1/2: 0.872 / Rpim(I) all: 0.2952 / Rrim(I) all: 1.095

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5084refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→30.5 Å / SU ML: 0.4035 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 29.7375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3082 222 10.01 %
Rwork0.272 1996 -
obs0.2762 2218 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.92 Å2
Refinement stepCycle: LAST / Resolution: 2.51→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 388 141 2 531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168583
X-RAY DIFFRACTIONf_angle_d1.8599879
X-RAY DIFFRACTIONf_chiral_restr0.119572
X-RAY DIFFRACTIONf_plane_restr0.0502104
X-RAY DIFFRACTIONf_dihedral_angle_d29.3082307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-3.160.41251110.3264995X-RAY DIFFRACTION99.82
3.16-30.50.28031110.25671001X-RAY DIFFRACTION98.41

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