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- PDB-8a34: MTH1 in complex with TH013071 -

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Basic information

Entry
Database: PDB / ID: 8a34
TitleMTH1 in complex with TH013071
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / NUDIX / inhibitor
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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity ...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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / 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 / nucleus / metal ion binding / cytoplasm / cytosol
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
ACETATE ION / 5-(2-phenylphenyl)-1H-pyrimidine-2,4-dione / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, H. / Scaletti, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: To Be Published
Title: MTH1 in complex with TH013071
Authors: Liu, H. / Scaletti, E. / Stenmark, P.
History
DepositionJun 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)37,67111
Polymers36,5072
Non-polymers1,1649
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-76 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.008, 68.714, 79.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 18253.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-KYI / 5-(2-phenylphenyl)-1H-pyrimidine-2,4-dione


Mass: 264.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12N2O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 18 % PEG6000, 0.1 M sodium acetate trihydrate pH 3.5, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→79.8 Å / Num. obs: 26050 / % possible obs: 99.1 % / Redundancy: 12.9 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1644 / CC1/2: 0.751

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zr0

3zr0


Resolution: 1.9→52.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.15 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26653 1249 4.8 %RANDOM
Rwork0.21695 ---
obs0.21941 24744 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.697 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---1.25 Å20 Å2
3---2.26 Å2
Refinement stepCycle: 1 / Resolution: 1.9→52.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 74 108 2727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192695
X-RAY DIFFRACTIONr_bond_other_d0.0020.022477
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9813647
X-RAY DIFFRACTIONr_angle_other_deg0.83535701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87124.211133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66415453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg161516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9873.9831265
X-RAY DIFFRACTIONr_mcbond_other1.9873.9831264
X-RAY DIFFRACTIONr_mcangle_it3.1215.9651580
X-RAY DIFFRACTIONr_mcangle_other3.125.9651581
X-RAY DIFFRACTIONr_scbond_it2.4344.291430
X-RAY DIFFRACTIONr_scbond_other2.3944.241407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8556.2432032
X-RAY DIFFRACTIONr_long_range_B_refined5.70631.3532909
X-RAY DIFFRACTIONr_long_range_B_other5.60631.2382888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 102 -
Rwork0.3 1814 -
obs--99.95 %

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