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- PDB-6jvt: Crystal structure of human MTH1 in complex with compound MI1030 -

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Basic information

Entry
Database: PDB / ID: 6jvt
TitleCrystal structure of human MTH1 in complex with compound MI1030
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / MTH1 / Oxidative DNA damage / 8-oxo-dGTP / Inhibitor development
Function / homology
Function and homology information


2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA protection / Phosphate bond hydrolysis by NUDT proteins / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to cadmium ion / acrosomal vesicle / male gonad development / nuclear membrane / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / extracellular space / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Chem-CJR / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsPeng, C. / Li, Y.H. / Cheng, Y.S.
CitationJournal: Bioorg.Chem. / Year: 2021
Title: Inhibitor development of MTH1 via high-throughput screening with fragment based library and MTH1 substrate binding cavity.
Authors: Peng, C. / Li, Y.H. / Yu, C.W. / Cheng, Z.H. / Liu, J.R. / Hsu, J.L. / Hsin, L.W. / Huang, C.T. / Juan, H.F. / Chern, J.W. / Cheng, Y.S.
History
DepositionApr 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7,8-dihydro-8-oxoguanine triphosphatase
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4724
Polymers35,9432
Non-polymers5292
Water6,089338
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2362
Polymers17,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2362
Polymers17,9711
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.204, 67.712, 79.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 3:13 or resseq 18:24 or resseq...
21(chain B and (resseq 3:13 or resseq 18:24 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 13
121(chain A and (resseq 3:13 or resseq 18:24 or resseq...A18 - 24
131(chain A and (resseq 3:13 or resseq 18:24 or resseq...A0
141(chain A and (resseq 3:13 or resseq 18:24 or resseq...A0
151(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 156
161(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 156
171(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 156
181(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 156
191(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 156
1101(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 156
1111(chain A and (resseq 3:13 or resseq 18:24 or resseq...A3 - 156
211(chain B and (resseq 3:13 or resseq 18:24 or resseq...B3 - 13
221(chain B and (resseq 3:13 or resseq 18:24 or resseq...B18 - 24
231(chain B and (resseq 3:13 or resseq 18:24 or resseq...B26 - 54
241(chain B and (resseq 3:13 or resseq 18:24 or resseq...B56 - 90
251(chain B and (resseq 3:13 or resseq 18:24 or resseq...B2 - 156
261(chain B and (resseq 3:13 or resseq 18:24 or resseq...B2 - 156
271(chain B and (resseq 3:13 or resseq 18:24 or resseq...B2 - 156
281(chain B and (resseq 3:13 or resseq 18:24 or resseq...B2 - 156
291(chain B and (resseq 3:13 or resseq 18:24 or resseq...B2 - 156
2101(chain B and (resseq 3:13 or resseq 18:24 or resseq...B2 - 156
2111(chain B and (resseq 3:13 or resseq 18:24 or resseq...B2 - 156

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Components

#1: Protein 7,8-dihydro-8-oxoguanine triphosphatase / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 17971.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-CJR / N4-methyl-6-[4-(oxetan-3-yl)piperazin-1-yl]pyrimidine-2,4-diamine


Mass: 264.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.84 % / Mosaicity: 0.496 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 3.75
Details: 30% PEG 6000, 200 mM Lithium sulphate, 100 mM Sodium acetate pH 3.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 2, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 30146 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.55 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.036 / Rrim(I) all: 0.075 / Χ2: 1.13 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.863.90.46428900.8220.2630.5350.88697.6
1.86-1.944.30.33129900.9120.1770.3770.96799.7
1.94-2.034.40.22729660.9530.1210.2581.01699.9
2.03-2.134.40.1629950.9760.0850.1821.06899.9
2.13-2.274.40.12130000.9860.0640.1371.05299.9
2.27-2.444.40.10329760.9910.0550.1171.06999.9
2.44-2.694.40.07230470.9950.0380.0821.08399.8
2.69-3.084.40.05130320.9970.0270.0581.06999.7
3.08-3.884.20.0430490.9980.0220.0461.59999.5
3.88-303.90.03132010.9980.0180.0361.49399

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→25.784 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.67
RfactorNum. reflection% reflection
Rfree0.2301 1945 6.67 %
Rwork0.1865 --
obs0.1894 29170 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.25 Å2 / Biso mean: 23.1269 Å2 / Biso min: 6.79 Å2
Refinement stepCycle: final / Resolution: 1.801→25.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 38 338 2852
Biso mean--30.77 32.49 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072580
X-RAY DIFFRACTIONf_angle_d0.8933486
X-RAY DIFFRACTIONf_chiral_restr0.059360
X-RAY DIFFRACTIONf_plane_restr0.006448
X-RAY DIFFRACTIONf_dihedral_angle_d12.0471504
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1336X-RAY DIFFRACTION7.494TORSIONAL
12B1336X-RAY DIFFRACTION7.494TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8011-1.84610.29861220.23491704182686
1.8461-1.8960.26981260.22311803192991
1.896-1.95180.25311390.21751858199794
1.9518-2.01480.28671350.19631898203396
2.0148-2.08680.23681370.19721928206597
2.0868-2.17030.24481410.18561958209998
2.1703-2.2690.22061390.18591959209897
2.269-2.38850.23681390.19051937207698
2.3885-2.53810.24371390.18981981212098
2.5381-2.73380.25381420.20181993213599
2.7338-3.00860.24411430.19781991213499
3.0086-3.4430.2321450.18182035218099
3.443-4.33450.18271440.15382032217699
4.3345-25.78660.21131540.18152148230299
Refinement TLS params.Method: refined / Origin x: 16.1729 Å / Origin y: 0.5171 Å / Origin z: -9.9965 Å
111213212223313233
T0.0899 Å2-0.0094 Å20.0039 Å2-0.0925 Å20.0062 Å2--0.0524 Å2
L0.8412 °20.0196 °20.059 °2-0.2302 °2-0.1195 °2---0.0315 °2
S0.0226 Å °-0.1182 Å °-0.126 Å °-0.0192 Å °-0.0077 Å °-0.0163 Å °-0.025 Å °-0.0142 Å °0.0144 Å °
Refinement TLS groupSelection details: all

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