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- PDB-7pox: TNKS2 in complex with OM-1700, treated with H2O2 -

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Basic information

Entry
Database: PDB / ID: 7pox
TitleTNKS2 in complex with OM-1700, treated with H2O2
ComponentsPoly [ADP-ribose] polymerase tankyrase-2
KeywordsTRANSFERASE / Zinc / coordination / enzyme / poly-adp-ribosylation / inhibitor / h2o2
Function / homology
Function and homology information


XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+-protein poly-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / 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 / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / : / 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 / : / 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
Similarity search - Domain/homology
Chem-N8K / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSowa, S.T. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063, 294085 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Open Biology / Year: 2022
Title: The zinc-binding motif in tankyrases is required for the structural integrity of the catalytic ADP-ribosyltransferase domain.
Authors: Sowa, S.T. / Lehtio, L.
History
DepositionSep 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Poly [ADP-ribose] polymerase tankyrase-2
BBB: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5734
Polymers49,6562
Non-polymers9172
Water57632
1
AAA: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, Protein is monomeric in size exclusion chromatography.
  • 25.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)25,2872
Polymers24,8281
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


  • defined by author&software
  • 25.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)25,2872
Polymers24,8281
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.640, 76.440, 147.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24828.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-N8K / N-[3-[5-(5-ethoxypyridin-2-yl)-4-(2-fluorophenyl)-1,2,4-triazol-3-yl]cyclobutyl]pyridine-2-carboxamide


Mass: 458.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23FN6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop / Details: PEG6000, Bicine, pH = 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16930 / % possible obs: 99.3 % / Redundancy: 13.3 % / CC1/2: 0.998 / Net I/σ(I): 10.64
Reflection shellResolution: 2.5→2.56 Å / Num. unique obs: 1255 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NOB

5nob


Resolution: 2.5→41.443 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.217 / SU B: 18.133 / SU ML: 0.356 / Average fsc free: 0.7962 / Average fsc work: 0.7921 / Cross valid method: FREE R-VALUE / ESU R: 0.629 / ESU R Free: 0.319
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2802 847 5.003 %
Rwork0.2479 16083 -
all0.25 --
obs-16930 99.331 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.444 Å20 Å20 Å2
2--7.655 Å2-0 Å2
3----7.211 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 68 32 3175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133267
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172966
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.6474403
X-RAY DIFFRACTIONr_angle_other_deg1.0551.5796818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.95721.244201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0615547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.41526
X-RAY DIFFRACTIONr_chiral_restr0.0350.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_nbd_refined0.1610.2477
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22602
X-RAY DIFFRACTIONr_nbtor_refined0.160.21475
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.211
X-RAY DIFFRACTIONr_nbd_other0.1520.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.24
X-RAY DIFFRACTIONr_mcbond_it1.9515.9261515
X-RAY DIFFRACTIONr_mcbond_other1.9485.9241514
X-RAY DIFFRACTIONr_mcangle_it3.5268.8571886
X-RAY DIFFRACTIONr_mcangle_other3.5258.861887
X-RAY DIFFRACTIONr_scbond_it1.3896.0031752
X-RAY DIFFRACTIONr_scbond_other1.3896.0021753
X-RAY DIFFRACTIONr_scangle_it2.5788.9422511
X-RAY DIFFRACTIONr_scangle_other2.5778.9412512
X-RAY DIFFRACTIONr_lrange_it5.04863.4713369
X-RAY DIFFRACTIONr_lrange_other5.04863.4653369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.382630.3941191X-RAY DIFFRACTION99.682
2.565-2.6350.355600.391139X-RAY DIFFRACTION100
2.635-2.7120.335570.4141086X-RAY DIFFRACTION99.8253
2.712-2.7950.359570.3281078X-RAY DIFFRACTION99.912
2.795-2.8870.287550.3191047X-RAY DIFFRACTION99.9093
2.887-2.9880.364540.3091041X-RAY DIFFRACTION99.8177
2.988-3.1010.228510.248964X-RAY DIFFRACTION100
3.101-3.2270.324510.237971X-RAY DIFFRACTION99.9023
3.227-3.3710.252470.233889X-RAY DIFFRACTION99.6805
3.371-3.5350.271460.254869X-RAY DIFFRACTION99.1333
3.535-3.7260.366400.28764X-RAY DIFFRACTION91.0532
3.726-3.9520.238410.239782X-RAY DIFFRACTION99.1566
3.952-4.2250.256400.18750X-RAY DIFFRACTION100
4.225-4.5630.198370.174702X-RAY DIFFRACTION100
4.563-4.9980.241330.18640X-RAY DIFFRACTION100
4.998-5.5870.233310.221592X-RAY DIFFRACTION100
5.587-6.450.439280.22532X-RAY DIFFRACTION100
6.45-7.8960.224250.19463X-RAY DIFFRACTION99.7955
7.896-11.150.265190.196364X-RAY DIFFRACTION100

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