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- PDB-6eq7: MTH1 in complex with fragment 11 -

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Basic information

Entry
Database: PDB / ID: 6eq7
TitleMTH1 in complex with fragment 11
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / Inhibitor / Complex / DNA repair / Fragment
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 / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-BS8 / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWiedmer, L. / Sledz, P. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
University of ZurichFK-16-032 Switzerland
Citation
Journal: Eur.J.Med.Chem. / Year: 2019
Title: Ligand retargeting by binding site analogy.
Authors: Wiedmer, L. / Scharer, C. / Spiliotopoulos, D. / Hurzeler, M. / Sledz, P. / Caflisch, A.
#1: Journal: Eur.J.Med.Chem. / Year: 2019
Title: Ligand retargeting by binding site analogy
Authors: Wiedmer, L. / Scharer, C. / Spiliotopoulos, D. / Hurzeler, M. / Sledz, P. / Caflisch, A.
History
DepositionOct 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Revision 1.3May 8, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4303
Polymers21,1051
Non-polymers3252
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.015, 60.592, 66.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-507-

HOH

31A-557-

HOH

41A-569-

HOH

51A-573-

HOH

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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: 21104.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-BS8 / 7-(3-fluoranylpyridin-4-yl)-1~{H}-imidazo[4,5-b]pyridin-2-amine


Mass: 229.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8FN5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 23 % PEG3350, 0.2 M LI2SO4, 0.1 M SODIUM ACETATE PH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 44725 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rrim(I) all: 0.028 / Net I/σ(I): 30.79
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 9.53 / Num. unique obs: 7090 / CC1/2: 0.986 / Rrim(I) all: 0.119 / % possible all: 98

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.738 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.85
RfactorNum. reflection% reflection
Rfree0.2042 2000 8.37 %
Rwork0.1747 --
obs0.1771 23890 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→44.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 22 273 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061374
X-RAY DIFFRACTIONf_angle_d0.8741878
X-RAY DIFFRACTIONf_dihedral_angle_d7.32775
X-RAY DIFFRACTIONf_chiral_restr0.086190
X-RAY DIFFRACTIONf_plane_restr0.006245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4994-1.53690.27481360.20281482X-RAY DIFFRACTION97
1.5369-1.57850.20641400.20211544X-RAY DIFFRACTION99
1.5785-1.62490.22851400.1951526X-RAY DIFFRACTION100
1.6249-1.67740.27061410.18781545X-RAY DIFFRACTION100
1.6774-1.73740.24591400.19251533X-RAY DIFFRACTION100
1.7374-1.80690.23121430.19391573X-RAY DIFFRACTION100
1.8069-1.88920.21111420.17891543X-RAY DIFFRACTION100
1.8892-1.98880.2421400.17681538X-RAY DIFFRACTION100
1.9888-2.11340.20411430.18141571X-RAY DIFFRACTION100
2.1134-2.27650.22081430.18121561X-RAY DIFFRACTION100
2.2765-2.50560.19281450.18141575X-RAY DIFFRACTION100
2.5056-2.86810.23521450.18841589X-RAY DIFFRACTION100
2.8681-3.61330.17431480.15351620X-RAY DIFFRACTION100
3.6133-44.7580.16831540.15651690X-RAY DIFFRACTION100

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