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- PDB-8a07: MTH1 in complex with TH001969 -

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Basic information

Entry
Database: PDB / ID: 8a07
TitleMTH1 in complex with TH001969
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 / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...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 / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 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 / 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
1~{H}-quinazoline-2,4-dione / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsScaletti, E.R. / Narwal, M. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: To Be Published
Title: MTH1 in complex with TH001969
Authors: Scaletti, E.R. / Narwal, M. / Stenmark, P.
History
DepositionMay 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 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)37,3129
Polymers36,5072
Non-polymers8057
Water2,198122
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 18.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)18,7045
Polymers18,2541
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


  • defined by author
  • 18.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)18,6084
Polymers18,2541
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.301, 67.420, 80.355
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-L3N / 1~{H}-quinazoline-2,4-dione


Mass: 162.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate trihydrate pH 3.5, 32 % PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.19→47.7 Å / Num. obs: 17261 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.985 / Net I/σ(I): 6.3
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 1428 / CC1/2: 0.556

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Processing

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

3zr0


Resolution: 2.19→47.7 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.59 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29185 848 4.9 %RANDOM
Rwork0.23556 ---
obs0.23828 16360 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.35 Å20 Å2
3---1.15 Å2
Refinement stepCycle: 1 / Resolution: 2.19→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 49 122 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192651
X-RAY DIFFRACTIONr_bond_other_d0.0010.022442
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9733593
X-RAY DIFFRACTIONr_angle_other_deg0.81435629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27124.328134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86415451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1111516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
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_it0.9352.5731250
X-RAY DIFFRACTIONr_mcbond_other0.9362.5721249
X-RAY DIFFRACTIONr_mcangle_it1.6743.8551566
X-RAY DIFFRACTIONr_mcangle_other1.6743.8561567
X-RAY DIFFRACTIONr_scbond_it0.8022.6581401
X-RAY DIFFRACTIONr_scbond_other0.7782.6121382
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3743.8821997
X-RAY DIFFRACTIONr_long_range_B_refined3.55419.5892830
X-RAY DIFFRACTIONr_long_range_B_other3.30519.522807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.242 Å
RfactorNum. reflection% reflection
Rfree0.366 71 -
Rwork0.3 1151 -
obs--96.6 %

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