PDB-5j42: Crystal structure of m2hTDP2-CAT in complex with a small molecule...

ID or keywords:

Entry

Database: PDB / ID: 5j42

Title

Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor

Components

Tyrosyl-DNA phosphodiesterase 2

Keywords

HYDROLASE / tyrosyl DNA phosphodiesterase 2 catalytic domain

Function / homology

Function and homology information

tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / aggresome / neuron development / PML body / double-strand break repair / single-stranded DNA binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Hornyak, P. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.

Funding support

United Kingdom, 3items

Citation

Journal: Biochem.J. / Year: 2016
Title: Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Authors: Hornyak, P. / Askwith, T. / Walker, S. / Komulainen, E. / Paradowski, M. / Pennicott, L.E. / Bartlett, E.J. / Brissett, N.C. / Raoof, A. / Watson, M. / Jordan, A.M. / Ogilvie, D.J. / Ward, S. ...

History

Deposition	Mar 31, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 6, 2016	Group: Database references
Revision 1.2	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3	Oct 16, 2019	Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5j42.cif.gz	232.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5j42.ent.gz	185.1 KB	Display	PDB format
PDBx/mmJSON format	5j42.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5j42_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5j42_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5j42_validation.xml.gz	30.6 KB	Display
Data in CIF	5j42_validation.cif.gz	46.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j4/5j42 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j42	HTTPS FTP

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Related structure data

Related structure data	5j3pC 5j3sC 5j3zC 4gyzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3vnd-5 4gyz-2 3vnd-7 6ez3-3 2pw6-d 5gwd-1 4q68-d 5yjp-d 5ufm-1 2wag-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#18 - Jun 2001 Myosin similarity (3) #19 - Jul 2001 Actin similarity (3) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Tyrosyl-DNA phosphodiesterase 2

B: Tyrosyl-DNA phosphodiesterase 2

hetero molecules

59.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tyrosyl-DNA phosphodiesterase 2

hetero molecules

defined by author
29.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tyrosyl-DNA phosphodiesterase 2

hetero molecules

defined by author
29.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.054, 42.872, 109.054
Angle α, β, γ (deg.)	90.00, 94.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Tyrosyl-DNA phosphodiesterase 2 / m2hTDP2-CAT / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA ...m2hTDP2-CAT / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / TRAF and TNF receptor-associated protein Mass: 28776.164 Da / Num. of mol.: 2 / Fragment: UNP residues 118-370 / Mutation: E242G, Q278R, Y231C, H323L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

#1: Protein

Tyrosyl-DNA phosphodiesterase 2 / m2hTDP2-CAT / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA ...

Mass: 28776.164 Da / Num. of mol.: 2 / Fragment: UNP residues 118-370 / Mutation: E242G, Q278R, Y231C, H323L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 6 types, 707 molecules

#2: Chemical	ChemComp-6FV / 10-(4-hydroxyphenyl)-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile Mass: 330.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₀N₄O₃
#3: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris propane pH 6.5, 0.2 M sodium tartrate, 20% w/v PEG3350, 0.3% v/v DMSO

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.7→42.07 Å / Num. obs: 112934 / % possible obs: 99.2 % / Redundancy: 3.1 % / CC_1/2: 1 / R_merge(I) obs: 0.043 / Net I/σ(I): 16.3
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 1 / CC_1/2: 0.6 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GYZ

4gyz

Resolution: 1.7→42.07 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 24.17

	R_factor	Num. reflection	% reflection
R_free	0.1969	5712	5.06 %
R_work	0.1603	-	-
obs	0.1622	112934	93.09 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.7→42.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3883	0	132	693	4708

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	4213
X-RAY DIFFRACTION	f_angle_d	1.654	5744
X-RAY DIFFRACTION	f_dihedral_angle_d	15.759	2644
X-RAY DIFFRACTION	f_chiral_restr	0.102	644
X-RAY DIFFRACTION	f_plane_restr	0.011	740

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 (%)
1.7-1.7193	0.3467	165	0.3438	3461	X-RAY DIFFRACTION	91
1.7193-1.7396	0.3564	186	0.3376	3563	X-RAY DIFFRACTION	92
1.7396-1.7608	0.4019	187	0.3533	3501	X-RAY DIFFRACTION	91
1.7608-1.7831	0.3834	193	0.3371	3547	X-RAY DIFFRACTION	90
1.7831-1.8065	0.3289	186	0.3233	3417	X-RAY DIFFRACTION	92
1.8065-1.8313	0.3642	144	0.3034	3518	X-RAY DIFFRACTION	91
1.8313-1.8574	0.329	214	0.297	3543	X-RAY DIFFRACTION	91
1.8574-1.8852	0.3376	169	0.2831	3464	X-RAY DIFFRACTION	92
1.8852-1.9146	0.3235	200	0.2712	3551	X-RAY DIFFRACTION	92
1.9146-1.946	0.275	177	0.2658	3416	X-RAY DIFFRACTION	89
1.946-1.9796	0.3411	176	0.2562	3422	X-RAY DIFFRACTION	90
1.9796-2.0155	0.3	203	0.2335	3530	X-RAY DIFFRACTION	92
2.0155-2.0543	0.2395	159	0.2096	3548	X-RAY DIFFRACTION	92
2.0543-2.0962	0.2765	164	0.1861	3549	X-RAY DIFFRACTION	92
2.0962-2.1418	0.2475	209	0.1807	3562	X-RAY DIFFRACTION	92
2.1418-2.1916	0.2124	192	0.165	3526	X-RAY DIFFRACTION	92
2.1916-2.2465	0.1868	199	0.1604	3584	X-RAY DIFFRACTION	93
2.2465-2.3072	0.2124	191	0.1561	3558	X-RAY DIFFRACTION	94
2.3072-2.3751	0.1829	183	0.1489	3619	X-RAY DIFFRACTION	93
2.3751-2.4517	0.1838	200	0.1443	3588	X-RAY DIFFRACTION	94
2.4517-2.5393	0.1721	219	0.1434	3671	X-RAY DIFFRACTION	95
2.5393-2.641	0.2038	197	0.1409	3719	X-RAY DIFFRACTION	96
2.641-2.7612	0.1695	212	0.1323	3658	X-RAY DIFFRACTION	96
2.7612-2.9067	0.1753	202	0.131	3690	X-RAY DIFFRACTION	97
2.9067-3.0888	0.1759	193	0.1346	3738	X-RAY DIFFRACTION	96
3.0888-3.3272	0.1624	204	0.1252	3602	X-RAY DIFFRACTION	96
3.3272-3.6618	0.1567	187	0.1273	3754	X-RAY DIFFRACTION	97
3.6618-4.1913	0.1428	220	0.1086	3639	X-RAY DIFFRACTION	95
4.1913-5.2789	0.1321	193	0.1151	3655	X-RAY DIFFRACTION	95
5.2789-42.083	0.1932	188	0.1608	3629	X-RAY DIFFRACTION	94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5578	0.3971	0.34	0.3648	0.1481	0.3138	-0.061	-0.1016	0.1545	0.111	0.0057	0.0991	-0.0545	-0.0961	0	0.1763	0.0191	0.0117	0.1844	-0.0097	0.2172	-21.8186	-0.6531	-43.5518
2	0.9768	-0.0301	0.3999	0.7367	-0.1319	0.7998	0.0384	-0.0536	-0.0786	-0.0074	-0.0034	0.0706	0.1039	0.0248	0.0001	0.1398	0.0049	0.0007	0.1283	0.0123	0.1766	-19.536	-11.4573	-51.9249
3	0.1165	-0.1025	-0.0434	0.2504	0.0856	0.0466	-0.0311	0.0425	-0.0623	-0.0815	-0.0558	-0.1372	0.2958	0.3045	-0.001	0.2015	0.0336	0.0021	0.2378	0.0135	0.2456	-3.1488	-17.5848	-48.2304
4	1.2759	0.087	0.3246	0.8939	-0.135	0.3459	-0.0006	-0.0646	0.0101	0.0175	-0.0346	-0.2033	0.0348	0.2544	0.0002	0.1442	-0.0036	0.0035	0.1696	0.0104	0.1628	-3.7442	-4.5752	-45.2845
5	0.3952	0.1185	0.2778	0.2909	0.1168	0.1993	0.0028	0.3262	0.0604	-0.2755	-0.0427	-0.1985	-0.0684	0.166	-0.003	0.1874	0.0103	0.0265	0.2429	0.0272	0.1658	-6.1715	-0.703	-56.0932
6	0.8422	0.3512	0.3896	0.5762	0.012	0.2328	-0.0084	0.063	0.2073	0.1091	0.0141	0.0833	-0.2054	-0.1871	0.0004	0.1922	0.0232	0.0163	0.1942	-0.0056	0.236	-14.977	3.4093	-44.8353
7	0.1372	-0.0846	-0.008	0.1979	0.111	0.0809	-0.1278	-0.0726	0.0359	-0.0526	0.0662	0.0144	0.0205	-0.1786	-0.0001	0.1962	-0.0024	-0.0052	0.2487	-0.0139	0.1683	-22.1682	-7.735	-9.7595
8	0.0956	-0.0023	-0.0548	0.0554	-0.0048	0.032	0.1023	0.0553	-0.0713	0.0147	0.0994	0.2271	0.0763	-0.1926	-0.0011	0.2109	-0.0346	-0.0177	0.2548	0.0105	0.2109	-29.9875	-10.9395	-12.0997
9	0.1091	0.008	-0.0066	0.3869	0.0716	0.0849	0.0241	-0.1332	0.0261	-0.0612	0.0576	0.2295	0.0714	-0.1131	-0.0002	0.2174	-0.001	0.0001	0.308	0.0274	0.2463	-27.6263	-2.8751	-7.6553
10	0.0746	-0.0835	-0.1316	0.0959	0.1471	0.2317	0.1283	-0.1533	0.1495	0.0481	-0.0051	0.3371	-0.1448	-0.2067	0.001	0.263	0.0306	0.0006	0.2932	0.002	0.2656	-25.7395	2.9525	-5.4008
11	0.1382	-0.1044	-0.1554	0.0812	0.119	0.1758	-0.0425	-0.2688	0.0041	0.1179	-0.0052	0.1353	-0.0701	-0.0772	-0.0005	0.2757	0.0011	0.0253	0.3293	0.0078	0.2224	-24.4141	0.0187	4.7397
12	0.4159	0.0369	0.1116	0.1068	0.0282	0.1395	-0.0575	-0.302	0.0521	0.1375	-0.042	0.1033	-0.0127	-0.037	-0.0229	0.2372	0.0084	-0.0084	0.2576	-0.0098	0.2222	-14.0018	4.6479	-2.5592
13	0.5522	-0.2545	0.2647	0.39	0.0344	0.277	-0.0523	-0.4469	-0.0341	0.2472	-0.0005	-0.0252	0.0837	0.0918	-0	0.2747	-0.0142	0.0119	0.3078	-0.0016	0.2327	-15.1653	-2.6815	1.1941
14	0.2654	-0.0514	0.075	0.235	-0.1355	0.1036	-0.0239	-0.0016	0.0873	0.0317	-0.0363	-0.195	-0.2981	0.1133	-0.0005	0.2118	-0.0186	-0.0374	0.1759	-0.0248	0.1895	-4.1021	1.3768	-3.0529
15	0.3464	-0.173	0.1479	0.2783	-0.1471	0.0994	-0.087	-0.2581	-0.1683	0.1079	-0.1042	-0.1535	-0.1148	0.2469	-0.0014	0.2608	-0.0145	-0.0206	0.3436	0.0258	0.2623	-6.5713	-5.5693	-1.0995
16	0.3564	-0.3017	0.1703	0.2688	-0.1221	0.1126	-0.0051	-0.002	-0.1465	0.0179	0.0105	-0.1326	0.1696	0.0825	0.0001	0.2161	-0.0044	-0.0507	0.2202	0.0068	0.2352	-6.3607	-15.65	0.6021
17	0.4482	0.0544	-0.2215	0.0795	-0.0304	0.1126	-0.0054	0.3239	-0.1924	-0.191	-0.1054	-0.0431	0.2592	0.2103	-0.0033	0.3285	0.026	0.0156	0.2859	-0.0387	0.2532	-11.4214	-13.2566	-18.9065
18	0.0786	-0.0824	-0.0331	0.1989	-0.018	0.0384	0.0783	-0.349	-0.1828	0.2759	-0.0105	0.048	0.1099	-0.2646	-0.0008	0.2618	-0.0303	-0.0069	0.309	0.0159	0.1895	-13.1031	-14.1471	3.699
19	0.4584	-0.1208	-0.0384	0.9228	-0.1097	0.0214	0.0188	-0.1234	-0.1331	-0.1017	0.0094	0.1019	0.3349	-0.1648	-0.0001	0.2333	-0.029	-0.0306	0.2352	-0.0044	0.1935	-21.3085	-14.3644	-9.3291

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 123 through 153 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 154 through 240 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 241 through 260 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 261 through 325 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 326 through 345 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 346 through 370 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 122 through 138 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 139 through 153 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 154 through 174 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 175 through 190 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 191 through 208 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 209 through 225 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 226 through 240 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 241 through 260 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 261 through 283 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 284 through 303 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 304 through 325 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 326 through 345 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 346 through 370 )

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Protein , 1 types, 2 molecules AB

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Movie

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Structure viewers

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Open data

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Assembly

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 707 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Yorodumi