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- PDB-3whw: MTH1 in complex with Ruthenium-based inhibitor -

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Basic information

Entry
Database: PDB / ID: 3whw
TitleMTH1 in complex with Ruthenium-based inhibitor
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MTH1 / organometallic inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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. / 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-RUX / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsStreib, M. / Kraeling, K. / Richter, K. / Steuber, H. / Meggers, E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: An Organometallic Inhibitor for the Human Repair Enzyme 7,8-Dihydro-8-oxoguanosine Triphosphatase.
Authors: Streib, M. / Kraeling, K. / Richter, K. / Xie, X. / Steuber, H. / Meggers, E.
History
DepositionSep 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)37,83511
Polymers35,9432
Non-polymers1,8929
Water61334
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8695
Polymers17,9711
Non-polymers8984
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)18,9656
Polymers17,9711
Non-polymers9945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.760, 67.650, 79.540
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: 17971.461 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RUX / [4-amino-2-methyl-6-(pyridin-2-yl-kappaN)quinazolin-7-yl-kappaC~7~](carbonyl){1-[(2,6-dimethoxyphenoxy)carbonyl]cyclopenta-2,4-dien-1-yl}ruthenium


Mass: 609.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H24N4O5Ru
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM P18 OF DATABASE P36639 (8ODP_HUMAN).

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: 26% PEG 6000, 100mM Naacetate, 100mM Li-sulphate, pH 4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2013
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.7→47.778 Å / Num. all: 9264 / Num. obs: 9264 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3 / Num. unique all: 1737 / Rsym value: 0.633 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZR1

3zr1


Resolution: 2.701→47.778 Å / SU ML: 0.36 / σ(F): 2 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 464 5.01 %random
Rwork0.2147 ---
all0.223 ---
obs0.2172 9260 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→47.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 113 34 2655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092712
X-RAY DIFFRACTIONf_angle_d1.283666
X-RAY DIFFRACTIONf_dihedral_angle_d12.923996
X-RAY DIFFRACTIONf_chiral_restr0.055364
X-RAY DIFFRACTIONf_plane_restr0.006466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.09-2.70120.36581510.28992871
3.092-3.89530.32591530.21722897
3.8953-47.78520.18921600.1813028
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0668-0.54710.01523.3293-0.65421.03080.08630.0628-0.0662-0.0404-0.08440.11640.0958-0.0014-0.01450.23950.0235-0.00580.2442-0.00980.34890.2172-22.611511.0163
26.53770.333-0.63242.46730.60191.24420.16090.601-1.09380.1554-0.0594-0.22830.20420.0916-0.05940.26020.0446-0.0760.2976-0.10.656128.6216-45.15238.5381
34.9889-0.1597-4.59180.4031-0.02884.4132-0.1901-0.3420.1543-0.0270.24720.0088-0.698-0.30080.24810.7344-0.01650.15270.5569-0.07680.3413-2.6641-23.803716.5102
42.01970.9675-0.27170.92941.38274.9474-0.6769-1.05240.8502-0.143-0.0920.15310.11210.31590.44970.4122-0.0566-0.24010.3980.03550.808732.4657-46.372713.805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 3:156
2X-RAY DIFFRACTION2CHAIN B AND RESID 3:156
3X-RAY DIFFRACTION3CHAIN A AND RESID 204:204
4X-RAY DIFFRACTION4CHAIN B AND RESID 205:205

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