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- PDB-7omc: Tankyrase 2 in complex with an inhibitor (OUL228) -

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Basic information

Entry
Database: PDB / ID: 7omc
TitleTankyrase 2 in complex with an inhibitor (OUL228)
Components(Poly [ADP-ribose] polymerase tankyrase- ...) x 2
KeywordsTRANSFERASE / Inhibitor / Enzyme
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 / 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 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-VJN / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSowa, S.T. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063, 294085 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs.
Authors: Maksimainen, M.M. / Murthy, S. / Sowa, S.T. / Galera-Prat, A. / Rolina, E. / Heiskanen, J.P. / Lehtio, L.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_common_name
Revision 1.2Jan 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)50,81813
Polymers49,6924
Non-polymers1,1269
Water3,801211
1
AAA: Poly [ADP-ribose] polymerase tankyrase-2
A: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4557
Polymers24,8462
Non-polymers6095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3636
Polymers24,8462
Non-polymers5174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.690, 98.180, 117.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-1363-

HOH

21BBB-1347-

HOH

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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, 220 molecules

#3: Chemical ChemComp-VJN / 8-propan-2-yloxy-4~{H}-thieno[2,3-c]isoquinolin-5-one


Mass: 259.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH=8.5, 200mM Lithium Sulphate, 20% PEG3350

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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 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 30936 / % possible obs: 99.95 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 22.06
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 3040 / CC1/2: 0.814

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Processing

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

5ows


Resolution: 2.1→49.138 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.164 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.19 / ESU R Free: 0.17
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2261 1547 5.001 %
Rwork0.1807 29388 -
all0.183 --
obs-30935 99.981 %
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: 50.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.405 Å2-0 Å20 Å2
2---2.273 Å2-0 Å2
3---2.678 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 62 211 3590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173145
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.6444720
X-RAY DIFFRACTIONr_angle_other_deg1.1441.5817236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24321.232211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97215573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1171528
X-RAY DIFFRACTIONr_chiral_restr0.0450.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02887
X-RAY DIFFRACTIONr_nbd_refined0.1780.2600
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.22896
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21594
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2228
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.214
X-RAY DIFFRACTIONr_nbd_other0.1630.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.210
X-RAY DIFFRACTIONr_mcbond_it2.3385.191664
X-RAY DIFFRACTIONr_mcbond_other2.3365.1881663
X-RAY DIFFRACTIONr_mcangle_it3.5637.7622075
X-RAY DIFFRACTIONr_mcangle_other3.5637.7642076
X-RAY DIFFRACTIONr_scbond_it2.555.491834
X-RAY DIFFRACTIONr_scbond_other2.5165.4761819
X-RAY DIFFRACTIONr_scangle_it4.0848.1272641
X-RAY DIFFRACTIONr_scangle_other4.0698.1032618
X-RAY DIFFRACTIONr_lrange_it6.09758.5733885
X-RAY DIFFRACTIONr_lrange_other6.06258.3773855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.3181130.2762151X-RAY DIFFRACTION100
2.155-2.2140.3021090.2552080X-RAY DIFFRACTION100
2.214-2.2780.3471070.2812031X-RAY DIFFRACTION99.9065
2.278-2.3480.2881040.2171968X-RAY DIFFRACTION100
2.348-2.4250.2651010.2021913X-RAY DIFFRACTION100
2.425-2.510.249980.1991875X-RAY DIFFRACTION100
2.51-2.6050.264950.1951806X-RAY DIFFRACTION100
2.605-2.7110.247910.221713X-RAY DIFFRACTION100
2.711-2.8310.264870.2021667X-RAY DIFFRACTION100
2.831-2.9690.275840.1931588X-RAY DIFFRACTION100
2.969-3.130.267800.1941524X-RAY DIFFRACTION100
3.13-3.320.275760.1791445X-RAY DIFFRACTION100
3.32-3.5490.173720.1661356X-RAY DIFFRACTION100
3.549-3.8330.21650.1661253X-RAY DIFFRACTION100
3.833-4.1980.182620.1591176X-RAY DIFFRACTION100
4.198-4.6930.156560.1311067X-RAY DIFFRACTION100
4.693-5.4170.181500.139949X-RAY DIFFRACTION100
5.417-6.6310.259430.202812X-RAY DIFFRACTION100
6.631-9.3630.195340.172637X-RAY DIFFRACTION100

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