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- PDB-9txw: Catalytic domain of human tankyrase 2 in complex with benzamide a... -

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Basic information

Entry
Database: PDB / ID: 9txw
TitleCatalytic domain of human tankyrase 2 in complex with benzamide adenine dinucleotide (BAD)
Components(Poly [ADP-ribose] polymerase tankyrase- ...) x 2
KeywordsTRANSFERASE / ADP-ribosylation / PARP / TNKS2
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / 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 / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / 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 / Wnt signaling pathway / protein polyubiquitination / Regulation of PTEN stability and activity / 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 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 repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-DQV / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPaakkonen, J. / Lehtio, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Replacement soaking for human tankyrase 2 enables studies on substrate analogues and inhibitors.
Authors: Paakkonen, J. / Sowa, S.T. / Bosetti, C. / Lehtio, L.
History
DepositionJan 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase tankyrase-2
C: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
D: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,51413
Polymers49,5784
Non-polymers1,9369
Water1,02757
1
A: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7096
Polymers24,7892
Non-polymers9204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-55 kcal/mol
Surface area10550 Å2
MethodPISA
2
C: Poly [ADP-ribose] polymerase tankyrase-2
D: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8057
Polymers24,7892
Non-polymers1,0165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-71 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.86, 76.61, 148.91
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A
21chain C
32chain B, fragment 1
42chain D, fragment 1
53chain B, fragment 2
63chain D, fragment 2

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPHEPHEAA951 - 11108 - 167
211SERSERPHEPHECB951 - 11108 - 167
322ALAALAARGARGBC1116 - 11283 - 15
422ALAALAARGARGDD1116 - 11283 - 15
533ALAALAGLUGLUBC1137 - 116124 - 48
633ALAALAGLUGLUDD1137 - 116124 - 48

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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

#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: 19352.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment L946-M1113 of catalytic domain L946-E1161 after cleavage with chymotrypsin
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-MBP / Production host: Escherichia coli BL21(DE3) (bacteria)
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: 5436.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment K1114-E1161 of catalytic domain L946-E1161 after cleavage with chymotrypsin
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pNIC-MBP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 4 types, 66 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DQV / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 662.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22% (w/v) PEG 3350, 0.2 M lithium sulfate, 0.1 M Tris, 1% (v/v) DMSO, 1 mM inhibitor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.3→74.455 Å / Num. obs: 22048 / % possible obs: 99.9 % / Redundancy: 40.3 % / Biso Wilson estimate: 38.2 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.348 / Rrim(I) all: 0.352 / Net I/σ(I): 13.29
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 39.8 % / Rmerge(I) obs: 1.988 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1598 / CC1/2: 0.837 / CC star: 0.955 / Rrim(I) all: 2.014 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MxCuBEdata collection
XDSJan 19, 2025data reduction
XSCALEJan 19, 2025data scaling
Coot0.9.8.93model building
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→74.455 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.026 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.363 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 2204 9.996 %Random selection
Rwork0.2023 19844 --
all0.206 ---
obs-22048 99.873 %-
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: 42.687 Å2
Baniso -1Baniso -2Baniso -3
1-1.917 Å20 Å20 Å2
2--1.086 Å2-0 Å2
3----3.003 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 115 57 3422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123484
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163069
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.8424713
X-RAY DIFFRACTIONr_angle_other_deg0.5211.7767066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.781530
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.25554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11210553
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.47210182
X-RAY DIFFRACTIONr_chiral_restr0.0670.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02880
X-RAY DIFFRACTIONr_nbd_refined0.2040.2606
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22687
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21627
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.211
X-RAY DIFFRACTIONr_nbd_other0.2840.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0870.27
X-RAY DIFFRACTIONr_mcbond_it3.5863.9851623
X-RAY DIFFRACTIONr_mcbond_other3.5743.9811619
X-RAY DIFFRACTIONr_mcangle_it5.7217.1292019
X-RAY DIFFRACTIONr_mcangle_other5.7127.1292018
X-RAY DIFFRACTIONr_scbond_it4.6654.6031861
X-RAY DIFFRACTIONr_scbond_other4.6634.6031862
X-RAY DIFFRACTIONr_scangle_it7.5268.2482690
X-RAY DIFFRACTIONr_scangle_other7.5258.2482691
X-RAY DIFFRACTIONr_lrange_it10.55341.1153729
X-RAY DIFFRACTIONr_lrange_other10.55940.9693724
X-RAY DIFFRACTIONr_ncsr_local_group_10.0560.0521959
X-RAY DIFFRACTIONr_ncsr_local_group_20.1030.051078
X-RAY DIFFRACTIONr_ncsr_local_group_30.0190.052957
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.056370.05008
12CX-RAY DIFFRACTIONLocal ncs0.056370.05008
23BX-RAY DIFFRACTIONLocal ncs0.103040.05006
24DX-RAY DIFFRACTIONLocal ncs0.103040.05006
35BX-RAY DIFFRACTIONLocal ncs0.019090.05007
36DX-RAY DIFFRACTIONLocal ncs0.019090.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3091600.2941435X-RAY DIFFRACTION99.8748
2.36-2.4240.3221570.2771395X-RAY DIFFRACTION100
2.424-2.4940.3091510.2671384X-RAY DIFFRACTION100
2.494-2.5710.2671430.2441319X-RAY DIFFRACTION99.8634
2.571-2.6550.3191450.2561291X-RAY DIFFRACTION100
2.655-2.7480.2671430.221234X-RAY DIFFRACTION99.7826
2.748-2.8520.2661300.1961202X-RAY DIFFRACTION99.8501
2.852-2.9680.2461320.211163X-RAY DIFFRACTION99.9228
2.968-3.10.2781240.2051122X-RAY DIFFRACTION99.9198
3.1-3.2510.2191200.1921087X-RAY DIFFRACTION99.9172
3.251-3.4260.2371110.1941010X-RAY DIFFRACTION99.8219
3.426-3.6340.2591070.2976X-RAY DIFFRACTION99.9078
3.634-3.8840.2091020.184921X-RAY DIFFRACTION100
3.884-4.1940.186970.166867X-RAY DIFFRACTION99.8964
4.194-4.5930.175880.152783X-RAY DIFFRACTION100
4.593-5.1330.171790.151732X-RAY DIFFRACTION100
5.133-5.9220.224740.183650X-RAY DIFFRACTION99.8621
5.922-7.2420.281610.207551X-RAY DIFFRACTION100
7.242-10.1930.265500.203443X-RAY DIFFRACTION99.596
10.193-74.4550.294300.314279X-RAY DIFFRACTION99.6774

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