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- PDB-5owt: Crystal structure of TNKS2 in complex with (5S)-5-methyl-5-[4-(4-... -

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Basic information

Entry
Database: PDB / ID: 5owt
TitleCrystal structure of TNKS2 in complex with (5S)-5-methyl-5-[4-(4-oxo-3,4-dihydroquinazolin-2-yl)phenyl]imidazolidine-2,4-dione
ComponentsTankyrase-2
KeywordsTRANSFERASE / Tankyrase / Inhibitor / ARTD6 / PARP5b / ADP-ribosyltransferase
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Regulation of PTEN stability and activity / Wnt signaling pathway / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-F37 / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNkizinkiko, Y. / Haikarainen, T. / Lehtio, L.
CitationJournal: Sci Rep / Year: 2018
Title: 2-Phenylquinazolinones as dual-activity tankyrase-kinase inhibitors.
Authors: Nkizinkiko, Y. / Desantis, J. / Koivunen, J. / Haikarainen, T. / Murthy, S. / Sancineto, L. / Massari, S. / Ianni, F. / Obaji, E. / Loza, M.I. / Pihlajaniemi, T. / Brea, J. / Tabarrini, O. / Lehtio, L.
History
DepositionSep 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,78310
Polymers54,6002
Non-polymers1,1848
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-77 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.000, 98.230, 113.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1359-

HOH

21B-1339-

HOH

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Components

#1: Protein Tankyrase-2 / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 27299.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-F37 / (5S)-5-methyl-5-[4-(4-oxidanylidene-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione


Mass: 334.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14N4O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 25529 / % possible obs: 99.9 % / Redundancy: 6.6 % / Net I/σ(I): 12.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3u9h

3u9h


Resolution: 2.2→19.18 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.866 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.202 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23698 1277 5 %RANDOM
Rwork0.1883 ---
obs0.19083 24253 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.728 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å20 Å2
2---2.28 Å2-0 Å2
3---3 Å2
Refinement stepCycle: 1 / Resolution: 2.2→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 72 136 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193467
X-RAY DIFFRACTIONr_bond_other_d0.0010.023163
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.9534679
X-RAY DIFFRACTIONr_angle_other_deg0.7883.0027254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49322.905179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1315569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2051528
X-RAY DIFFRACTIONr_chiral_restr0.2770.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02909
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2654.2681644
X-RAY DIFFRACTIONr_mcbond_other3.264.2661643
X-RAY DIFFRACTIONr_mcangle_it4.9356.3832049
X-RAY DIFFRACTIONr_mcangle_other4.9346.3852050
X-RAY DIFFRACTIONr_scbond_it3.8564.6191823
X-RAY DIFFRACTIONr_scbond_other3.8554.6181824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7976.7962628
X-RAY DIFFRACTIONr_long_range_B_refined9.24940.31214831
X-RAY DIFFRACTIONr_long_range_B_other9.24640.31214780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 92 -
Rwork0.311 1749 -
obs--99.95 %

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