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- PDB-6eq4: MTH1 in complex with fragment 8 -

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Basic information

Entry
Database: PDB / ID: 6eq4
TitleMTH1 in complex with fragment 8
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 / 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 / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-BSW / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)21,5104
Polymers21,1051
Non-polymers4053
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-17 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.673, 65.939, 35.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

21A-500-

HOH

31A-602-

HOH

41A-605-

HOH

51A-608-

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 (bacteria)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-BSW / 4-(3-fluoranylpyridin-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine


Mass: 213.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8FN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 1.7 Å3/Da / Density % sol: 27.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 23 % PEG3350, 0.2 M LI2SO4, 0.1 M SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 54076 / % possible obs: 98.4 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rrim(I) all: 0.059 / Net I/σ(I): 18.96
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.11 % / Mean I/σ(I) obs: 10.99 / Num. unique obs: 8674 / CC1/2: 0.987 / Rrim(I) all: 0.095 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.887 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 17.75
RfactorNum. reflection% reflection
Rfree0.1874 1998 6.93 %
Rwork0.1663 --
obs0.1678 28836 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→35.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 26 308 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091370
X-RAY DIFFRACTIONf_angle_d1.0321869
X-RAY DIFFRACTIONf_dihedral_angle_d6.3631059
X-RAY DIFFRACTIONf_chiral_restr0.089188
X-RAY DIFFRACTIONf_plane_restr0.008245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3988-1.43380.20961290.19561867X-RAY DIFFRACTION98
1.4338-1.47260.22051450.17961890X-RAY DIFFRACTION100
1.4726-1.51590.21631300.17171894X-RAY DIFFRACTION100
1.5159-1.56480.19831490.16731925X-RAY DIFFRACTION100
1.5648-1.62070.17271540.16241865X-RAY DIFFRACTION99
1.6207-1.68560.19461330.16851927X-RAY DIFFRACTION99
1.6856-1.76240.2241420.171881X-RAY DIFFRACTION99
1.7624-1.85530.21071380.16661928X-RAY DIFFRACTION100
1.8553-1.97150.18561480.15691911X-RAY DIFFRACTION99
1.9715-2.12370.1681430.1671911X-RAY DIFFRACTION99
2.1237-2.33740.1991440.1611925X-RAY DIFFRACTION99
2.3374-2.67550.19271430.1711921X-RAY DIFFRACTION98
2.6755-3.37050.15771450.16221969X-RAY DIFFRACTION99
3.3705-35.89880.18421550.16522024X-RAY DIFFRACTION97

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