PDB-9txt: Catalytic domain of human tankyrase 2 in complex with a dual-site...

ID or keywords:

Entry

Database: PDB / ID: 9txt

Title

Catalytic domain of human tankyrase 2 in complex with a dual-site inhibitor

Components

(Poly [ADP-ribose] polymerase tankyrase- ...) x 2

Keywords

TRANSFERASE / ADP-ribosylation / Inhibitor / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Paakkonen, J. / Lehtio, L.

Funding support

Finland, 1items

Citation

Journal: 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

Deposition	Jan 16, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9txt.cif.gz	102 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/9txt ftp://data.pdbj.org/pub/pdb/validation_reports/tx/9txt	HTTPS FTP

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Related structure data

Related structure data	9txuC 9txvC 9txwC 7ojo 8b6m C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15151/ESRF-ES-1309325308 / Data set type: diffraction image data Metadata reference: 10.23729/ee61d6dd-5100-4fee-bb21-bf78050d240c

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

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

51.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Poly [ADP-ribose] polymerase tankyrase-2

B: Poly [ADP-ribose] polymerase tankyrase-2

hetero molecules

defined by author
Evidence: gel filtration, The catalytic domain itself is monomeric but here consists of two fragments after cleavage with chymotrypsin.
25.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Poly [ADP-ribose] polymerase tankyrase-2

D: Poly [ADP-ribose] polymerase tankyrase-2

hetero molecules

defined by author
Evidence: gel filtration, The catalytic domain itself is monomeric but here consists of two fragments after cleavage with chymotrypsin.
25.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.71, 76.3, 148.98
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	chain A
2	1	chain C
3	2	chain B, fragment 1
4	2	chain D, fragment 1
5	3	chain B, fragment 2
6	3	chain D, fragment 2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	PHE	PHE	A	A	952 - 1110	9 - 167
2	1	1	GLY	GLY	PHE	PHE	C	B	952 - 1110	9 - 167
3	2	2	ALA	ALA	GLY	GLY	B	C	1116 - 1127	3 - 14
4	2	2	ALA	ALA	GLY	GLY	D	D	1116 - 1127	3 - 14
5	3	3	LEU	LEU	GLU	GLU	B	C	1136 - 1161	23 - 48
6	3	3	LEU	LEU	GLU	GLU	D	D	1136 - 1161	23 - 48

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

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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

#1: Protein

Poly [ADP-ribose] polymerase tankyrase-2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / 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 ...

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, 17 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-OY6 / ~{N}-(2-methoxyphenyl)-4-[[2-(4-oxidanylidene-3~{H}-quinazolin-2-yl)ethyl-(thiophen-2-ylmethyl)carbamoyl]amino]benzamide Mass: 553.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₀H₂₇N₅O₄S / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.7 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96546 Å / Relative weight: 1
Reflection	Resolution: 2.8→41.62 Å / Num. obs: 12297 / % possible obs: 99.8 % / Redundancy: 15.6 % / B_iso Wilson estimate: 42.4 Å² / CC_1/2: 0.995 / CC star: 0.999 / R_merge(I) obs: 0.232 / R_rim(I) all: 0.24 / Net I/σ(I): 11.11
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 8.7 % / R_merge(I) obs: 1.132 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 883 / CC_1/2: 0.74 / CC star: 0.922 / R_rim(I) all: 1.204 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
XDS	Jun 30, 2023	data reduction
XSCALE	Jun 30, 2023	data scaling
Coot	0.9.8.93	model building
PHASER	2.8.3	phasing
REFMAC	5.8.0425	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→41.62 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.909 / SU B: 14.601 / SU ML: 0.278 / Cross valid method: FREE R-VALUE / ESU R Free: 0.385
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2409	1227	9.978 %	Random selection
R_work	0.1967	11070	-	-
all	0.201	-	-	-
obs	-	12297	99.765 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 47.212 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.776 Å²	0 Å²	0 Å²
2-	-	1.817 Å²	-0 Å²
3-	-	-	-4.593 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→41.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3232	0	107	8	3347

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	3450
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	3051
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	1.871	4652
X-RAY DIFFRACTION	r_angle_other_deg	0.557	1.802	7013
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.893	5	404
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.366	5	27
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.16	10	546
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.287	10	179
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	452
X-RAY DIFFRACTION	r_chiral_restr_other	0.027	0.2	8
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4128
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	884
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	598
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	2884
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	1646
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1775
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.115	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.036	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.217	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.207	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.114	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	3.645	4.668	1613
X-RAY DIFFRACTION	r_mcbond_other	3.644	4.668	1613
X-RAY DIFFRACTION	r_mcangle_it	5.962	8.376	2009
X-RAY DIFFRACTION	r_mcangle_other	5.96	8.377	2010
X-RAY DIFFRACTION	r_scbond_it	3.932	4.844	1837
X-RAY DIFFRACTION	r_scbond_other	3.931	4.844	1838
X-RAY DIFFRACTION	r_scangle_it	6.263	8.72	2640
X-RAY DIFFRACTION	r_scangle_other	6.262	8.719	2641
X-RAY DIFFRACTION	r_lrange_it	9.572	44.821	3737
X-RAY DIFFRACTION	r_lrange_other	9.571	44.816	3738
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	21752
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.007	0.05	971
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.088	0.05	2745

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07575	0.05008
1	2	C	X-RAY DIFFRACTION	Local ncs	0.07575	0.05008
2	3	B	X-RAY DIFFRACTION	Local ncs	0.00704	0.05008
2	4	D	X-RAY DIFFRACTION	Local ncs	0.00704	0.05008
3	5	B	X-RAY DIFFRACTION	Local ncs	0.08804	0.05007
3	6	D	X-RAY DIFFRACTION	Local ncs	0.08804	0.05007

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.8-2.872	0.322	88	0.336	788	X-RAY DIFFRACTION	99.5455
2.872-2.951	0.349	86	0.287	772	X-RAY DIFFRACTION	99.8836
2.951-3.036	0.342	81	0.267	769	X-RAY DIFFRACTION	99.8825
3.036-3.129	0.26	81	0.22	724	X-RAY DIFFRACTION	100
3.129-3.23	0.251	84	0.207	740	X-RAY DIFFRACTION	100
3.23-3.343	0.295	74	0.211	677	X-RAY DIFFRACTION	99.867
3.343-3.469	0.287	75	0.219	685	X-RAY DIFFRACTION	99.3464
3.469-3.609	0.224	68	0.181	624	X-RAY DIFFRACTION	99.4253
3.609-3.768	0.212	71	0.175	632	X-RAY DIFFRACTION	99.858
3.768-3.951	0.186	67	0.165	588	X-RAY DIFFRACTION	100
3.951-4.162	0.187	65	0.149	582	X-RAY DIFFRACTION	99.8457
4.162-4.412	0.168	58	0.157	526	X-RAY DIFFRACTION	100
4.412-4.713	0.199	58	0.154	519	X-RAY DIFFRACTION	100
4.713-5.085	0.206	54	0.15	484	X-RAY DIFFRACTION	99.6296
5.085-5.562	0.257	49	0.181	439	X-RAY DIFFRACTION	99.7955
5.562-6.205	0.297	45	0.2	412	X-RAY DIFFRACTION	100
6.205-7.138	0.242	41	0.201	365	X-RAY DIFFRACTION	100
7.138-8.679	0.249	35	0.194	319	X-RAY DIFFRACTION	99.7183
8.679-12.016	0.232	28	0.192	252	X-RAY DIFFRACTION	99.6441
12.016-41.62	0.28	19	0.349	173	X-RAY DIFFRACTION	99.4819

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

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Non-polymers , 4 types, 17 molecules

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