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- PDB-7ojo: Tankyrase 2 in complex with two small molecule fragments -

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Basic information

Entry
Database: PDB / ID: 7ojo
TitleTankyrase 2 in complex with two small molecule fragments
Components(Poly [ADP-ribose] polymerase tankyrase- ...) x 2
KeywordsTRANSFERASE / Inhibitor / Complex / Poly-ADP-ribosylation / Enzyme
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 / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+ 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 / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+ 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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / Ankyrin repeats (many copies) / 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 (many copies) / 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
4-acetamido-~{N}-(2-methoxyphenyl)benzamide / quinazolin-4(3H)-one / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSowa, S.T. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063, 294085 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: To Be Published
Title: Tankyrase 2 in complex with an inhibitor (OM-153)
Authors: Sowa, S.T. / Lehtio, L.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 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
A: Poly [ADP-ribose] polymerase tankyrase-2
BBB: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,26016
Polymers49,6924
Non-polymers1,56812
Water2,684149
1
AAA: Poly [ADP-ribose] polymerase tankyrase-2
A: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


  • defined by author
  • Evidence: gel filtration, Protein is monomeric in solution.
  • 25.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)25,5347
Polymers24,8462
Non-polymers6885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


  • defined by author
  • 25.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)25,7269
Polymers24,8462
Non-polymers8807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.645, 76.386, 148.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111AAA952 - 1161
221BBB952 - 1161

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Poly [ADP-ribose] polymerase tankyrase- ... , 2 types, 4 molecules AAABBBAB

#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: 19482.053 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: Protein/peptide 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: 5364.037 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

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Non-polymers , 5 types, 161 molecules

#3: Chemical ChemComp-WQG / quinazolin-4(3H)-one


Mass: 146.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VGZ / 4-acetamido-~{N}-(2-methoxyphenyl)benzamide


Mass: 284.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris pH=8.5, 200 mM Li2SO4, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.3→148.88 Å / Num. obs: 21934 / % possible obs: 99.9 % / Redundancy: 24.4 % / CC1/2: 0.981 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 2067 / CC1/2: 0.728

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NOB

5nob


Resolution: 2.3→74.549 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.862 / SU B: 8.75 / SU ML: 0.201 / Cross valid method: FREE R-VALUE / ESU R: 0.388 / ESU R Free: 0.266
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2769 1107 5.061 %
Rwork0.232 20766 -
all0.234 --
obs-21873 99.963 %
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: 15.737 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2--0.273 Å2-0 Å2
3----3.543 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 96 149 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133417
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173040
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.6444605
X-RAY DIFFRACTIONr_angle_other_deg1.0981.586972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.755404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.58321.188202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14315546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251527
X-RAY DIFFRACTIONr_chiral_restr0.0420.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023930
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
X-RAY DIFFRACTIONr_nbd_refined0.160.2594
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.22817
X-RAY DIFFRACTIONr_nbtor_refined0.160.21547
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.21520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2162
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.222
X-RAY DIFFRACTIONr_nbd_other0.2210.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.216
X-RAY DIFFRACTIONr_mcbond_it1.1021.6961622
X-RAY DIFFRACTIONr_mcbond_other1.1021.6971621
X-RAY DIFFRACTIONr_mcangle_it2.0832.5342021
X-RAY DIFFRACTIONr_mcangle_other2.0822.5342022
X-RAY DIFFRACTIONr_scbond_it0.6141.7171795
X-RAY DIFFRACTIONr_scbond_other0.5971.6871772
X-RAY DIFFRACTIONr_scangle_it1.1852.5522583
X-RAY DIFFRACTIONr_scangle_other1.1822.5062548
X-RAY DIFFRACTIONr_lrange_it3.75418.643696
X-RAY DIFFRACTIONr_lrange_other3.71818.6413679
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.056356
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.078860.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.078860.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.365780.3121498X-RAY DIFFRACTION99.6207
2.36-2.4250.349770.3071479X-RAY DIFFRACTION100
2.425-2.4950.33690.2751413X-RAY DIFFRACTION100
2.495-2.5720.299760.251407X-RAY DIFFRACTION100
2.572-2.6560.273600.2471348X-RAY DIFFRACTION100
2.656-2.7490.308640.2521327X-RAY DIFFRACTION100
2.749-2.8530.3750.2281228X-RAY DIFFRACTION100
2.853-2.9690.282660.2291245X-RAY DIFFRACTION100
2.969-3.1010.264610.231159X-RAY DIFFRACTION100
3.101-3.2530.248610.2241121X-RAY DIFFRACTION100
3.253-3.4280.225700.2171067X-RAY DIFFRACTION100
3.428-3.6360.219510.2021025X-RAY DIFFRACTION100
3.636-3.8870.231480.199955X-RAY DIFFRACTION99.9004
3.887-4.1980.193460.175913X-RAY DIFFRACTION100
4.198-4.5990.201480.175824X-RAY DIFFRACTION100
4.599-5.1410.274420.194756X-RAY DIFFRACTION100
5.141-5.9350.36460.239673X-RAY DIFFRACTION100
5.935-7.2660.339280.267578X-RAY DIFFRACTION100
7.266-10.2630.268260.21469X-RAY DIFFRACTION100

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