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

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Basic information

Entry
Database: PDB / ID: 5j42
TitleCrystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor
ComponentsTyrosyl-DNA phosphodiesterase 2
KeywordsHYDROLASE / 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 ...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 / manganese ion binding / endonuclease activity / nucleolus / magnesium ion binding / cytoplasm
Similarity search - Function
: / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6FV / : / L(+)-TARTARIC ACID / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHornyak, P. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
Cancer Research UKC6563/A16771 United Kingdom
Cancer Research UKC480/A11411 United Kingdom
CitationJournal: 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. ...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.E. / Atack, J.R. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.4Jan 10, 2024Group: 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,53216
Polymers57,5522
Non-polymers1,97914
Water12,484693
1
A: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6167
Polymers28,7761
Non-polymers8406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9169
Polymers28,7761
Non-polymers1,1408
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number4
Space group name H-MP1211

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Components

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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

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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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Details

Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→42.07 Å / Num. obs: 112934 / % possible obs: 99.2 % / Redundancy: 3.1 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1 / CC1/2: 0.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1969 5712 5.06 %
Rwork0.1603 --
obs0.1622 112934 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 132 693 4708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024213
X-RAY DIFFRACTIONf_angle_d1.6545744
X-RAY DIFFRACTIONf_dihedral_angle_d15.7592644
X-RAY DIFFRACTIONf_chiral_restr0.102644
X-RAY DIFFRACTIONf_plane_restr0.011740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.34671650.34383461X-RAY DIFFRACTION91
1.7193-1.73960.35641860.33763563X-RAY DIFFRACTION92
1.7396-1.76080.40191870.35333501X-RAY DIFFRACTION91
1.7608-1.78310.38341930.33713547X-RAY DIFFRACTION90
1.7831-1.80650.32891860.32333417X-RAY DIFFRACTION92
1.8065-1.83130.36421440.30343518X-RAY DIFFRACTION91
1.8313-1.85740.3292140.2973543X-RAY DIFFRACTION91
1.8574-1.88520.33761690.28313464X-RAY DIFFRACTION92
1.8852-1.91460.32352000.27123551X-RAY DIFFRACTION92
1.9146-1.9460.2751770.26583416X-RAY DIFFRACTION89
1.946-1.97960.34111760.25623422X-RAY DIFFRACTION90
1.9796-2.01550.32030.23353530X-RAY DIFFRACTION92
2.0155-2.05430.23951590.20963548X-RAY DIFFRACTION92
2.0543-2.09620.27651640.18613549X-RAY DIFFRACTION92
2.0962-2.14180.24752090.18073562X-RAY DIFFRACTION92
2.1418-2.19160.21241920.1653526X-RAY DIFFRACTION92
2.1916-2.24650.18681990.16043584X-RAY DIFFRACTION93
2.2465-2.30720.21241910.15613558X-RAY DIFFRACTION94
2.3072-2.37510.18291830.14893619X-RAY DIFFRACTION93
2.3751-2.45170.18382000.14433588X-RAY DIFFRACTION94
2.4517-2.53930.17212190.14343671X-RAY DIFFRACTION95
2.5393-2.6410.20381970.14093719X-RAY DIFFRACTION96
2.641-2.76120.16952120.13233658X-RAY DIFFRACTION96
2.7612-2.90670.17532020.1313690X-RAY DIFFRACTION97
2.9067-3.08880.17591930.13463738X-RAY DIFFRACTION96
3.0888-3.32720.16242040.12523602X-RAY DIFFRACTION96
3.3272-3.66180.15671870.12733754X-RAY DIFFRACTION97
3.6618-4.19130.14282200.10863639X-RAY DIFFRACTION95
4.1913-5.27890.13211930.11513655X-RAY DIFFRACTION95
5.2789-42.0830.19321880.16083629X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL11 (°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)
10.55780.39710.340.36480.14810.3138-0.061-0.10160.15450.1110.00570.0991-0.0545-0.096100.17630.01910.01170.1844-0.00970.2172-21.8186-0.6531-43.5518
20.9768-0.03010.39990.7367-0.13190.79980.0384-0.0536-0.0786-0.0074-0.00340.07060.10390.02480.00010.13980.00490.00070.12830.01230.1766-19.536-11.4573-51.9249
30.1165-0.1025-0.04340.25040.08560.0466-0.03110.0425-0.0623-0.0815-0.0558-0.13720.29580.3045-0.0010.20150.03360.00210.23780.01350.2456-3.1488-17.5848-48.2304
41.27590.0870.32460.8939-0.1350.3459-0.0006-0.06460.01010.0175-0.0346-0.20330.03480.25440.00020.1442-0.00360.00350.16960.01040.1628-3.7442-4.5752-45.2845
50.39520.11850.27780.29090.11680.19930.00280.32620.0604-0.2755-0.0427-0.1985-0.06840.166-0.0030.18740.01030.02650.24290.02720.1658-6.1715-0.703-56.0932
60.84220.35120.38960.57620.0120.2328-0.00840.0630.20730.10910.01410.0833-0.2054-0.18710.00040.19220.02320.01630.1942-0.00560.236-14.9773.4093-44.8353
70.1372-0.0846-0.0080.19790.1110.0809-0.1278-0.07260.0359-0.05260.06620.01440.0205-0.1786-0.00010.1962-0.0024-0.00520.2487-0.01390.1683-22.1682-7.735-9.7595
80.0956-0.0023-0.05480.0554-0.00480.0320.10230.0553-0.07130.01470.09940.22710.0763-0.1926-0.00110.2109-0.0346-0.01770.25480.01050.2109-29.9875-10.9395-12.0997
90.10910.008-0.00660.38690.07160.08490.0241-0.13320.0261-0.06120.05760.22950.0714-0.1131-0.00020.2174-0.0010.00010.3080.02740.2463-27.6263-2.8751-7.6553
100.0746-0.0835-0.13160.09590.14710.23170.1283-0.15330.14950.0481-0.00510.3371-0.1448-0.20670.0010.2630.03060.00060.29320.0020.2656-25.73952.9525-5.4008
110.1382-0.1044-0.15540.08120.1190.1758-0.0425-0.26880.00410.1179-0.00520.1353-0.0701-0.0772-0.00050.27570.00110.02530.32930.00780.2224-24.41410.01874.7397
120.41590.03690.11160.10680.02820.1395-0.0575-0.3020.05210.1375-0.0420.1033-0.0127-0.037-0.02290.23720.0084-0.00840.2576-0.00980.2222-14.00184.6479-2.5592
130.5522-0.25450.26470.390.03440.277-0.0523-0.4469-0.03410.2472-0.0005-0.02520.08370.0918-00.2747-0.01420.01190.3078-0.00160.2327-15.1653-2.68151.1941
140.2654-0.05140.0750.235-0.13550.1036-0.0239-0.00160.08730.0317-0.0363-0.195-0.29810.1133-0.00050.2118-0.0186-0.03740.1759-0.02480.1895-4.10211.3768-3.0529
150.3464-0.1730.14790.2783-0.14710.0994-0.087-0.2581-0.16830.1079-0.1042-0.1535-0.11480.2469-0.00140.2608-0.0145-0.02060.34360.02580.2623-6.5713-5.5693-1.0995
160.3564-0.30170.17030.2688-0.12210.1126-0.0051-0.002-0.14650.01790.0105-0.13260.16960.08250.00010.2161-0.0044-0.05070.22020.00680.2352-6.3607-15.650.6021
170.44820.0544-0.22150.0795-0.03040.1126-0.00540.3239-0.1924-0.191-0.1054-0.04310.25920.2103-0.00330.32850.0260.01560.2859-0.03870.2532-11.4214-13.2566-18.9065
180.0786-0.0824-0.03310.1989-0.0180.03840.0783-0.349-0.18280.2759-0.01050.0480.1099-0.2646-0.00080.2618-0.0303-0.00690.3090.01590.1895-13.1031-14.14713.699
190.4584-0.1208-0.03840.9228-0.10970.02140.0188-0.1234-0.1331-0.10170.00940.10190.3349-0.1648-0.00010.2333-0.029-0.03060.2352-0.00440.1935-21.3085-14.3644-9.3291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 123 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 240 )
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 260 )
4X-RAY DIFFRACTION4chain 'A' and (resid 261 through 325 )
5X-RAY DIFFRACTION5chain 'A' and (resid 326 through 345 )
6X-RAY DIFFRACTION6chain 'A' and (resid 346 through 370 )
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 138 )
8X-RAY DIFFRACTION8chain 'B' and (resid 139 through 153 )
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 174 )
10X-RAY DIFFRACTION10chain 'B' and (resid 175 through 190 )
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 208 )
12X-RAY DIFFRACTION12chain 'B' and (resid 209 through 225 )
13X-RAY DIFFRACTION13chain 'B' and (resid 226 through 240 )
14X-RAY DIFFRACTION14chain 'B' and (resid 241 through 260 )
15X-RAY DIFFRACTION15chain 'B' and (resid 261 through 283 )
16X-RAY DIFFRACTION16chain 'B' and (resid 284 through 303 )
17X-RAY DIFFRACTION17chain 'B' and (resid 304 through 325 )
18X-RAY DIFFRACTION18chain 'B' and (resid 326 through 345 )
19X-RAY DIFFRACTION19chain 'B' and (resid 346 through 370 )

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