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- PDB-7nr6: Structure of NUDT15 in complex with NSC56456 -

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Basic information

Entry
Database: PDB / ID: 7nr6
TitleStructure of NUDT15 in complex with NSC56456
ComponentsProbable 8-oxo-dGTP diphosphatase NUDT15
KeywordsHYDROLASE / Inhibitor / complex / Nucleoside Triphosphate Pyrophosphohydrolase
Function / homology
Function and homology information


nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins ...nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins / DNA protection / Azathioprine ADME / xenobiotic catabolic process / regulation of proteasomal protein catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol
Similarity search - Function
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
2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione / Nucleotide triphosphate diphosphatase NUDT15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRehling, D. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
CitationJournal: To Be Published
Title: Coupling cellular target engagement to drug-induced responses with CeTEAM
Authors: Valerie, N.C.K. / Rehling, D. / Stenmark, P.
History
DepositionMar 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable 8-oxo-dGTP diphosphatase NUDT15
B: Probable 8-oxo-dGTP diphosphatase NUDT15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9418
Polymers37,2702
Non-polymers6716
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-24 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.843, 49.032, 135.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Probable 8-oxo-dGTP diphosphatase NUDT15 / 8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / ...8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / Nucleoside diphosphate-linked moiety X motif 15 / Nudix motif 15


Mass: 18635.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT15, MTH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NV35, nucleotide diphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UO8 / 2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione


Mass: 249.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2M sodium acetate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→67.69 Å / Num. obs: 29634 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.919 / Num. unique obs: 1714 / CC1/2: 0.757 / Rpim(I) all: 0.371 / Rrim(I) all: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BON

5bon


Resolution: 1.8→67.69 Å / SU ML: 0.1893 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 1419 4.81 %
Rwork0.1872 28109 -
obs0.1882 29528 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 44 284 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572629
X-RAY DIFFRACTIONf_angle_d0.82243575
X-RAY DIFFRACTIONf_chiral_restr0.061357
X-RAY DIFFRACTIONf_plane_restr0.0055494
X-RAY DIFFRACTIONf_dihedral_angle_d13.5813975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.29581300.24732767X-RAY DIFFRACTION99.52
1.86-1.940.27981430.23132766X-RAY DIFFRACTION99.11
1.94-2.030.22591480.21432731X-RAY DIFFRACTION99
2.03-2.130.24631190.19942828X-RAY DIFFRACTION99.83
2.13-2.270.22021260.20542793X-RAY DIFFRACTION99.83
2.27-2.440.241370.20922796X-RAY DIFFRACTION99.19
2.44-2.690.21591500.20612780X-RAY DIFFRACTION99.49
2.69-3.080.21311540.20332837X-RAY DIFFRACTION99.67
3.08-3.880.1951450.16132861X-RAY DIFFRACTION99.34
3.88-67.690.17091670.16382950X-RAY DIFFRACTION98.39
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)
13.253242045431.13150392018-0.4258774066711.520779577580.6053697113282.077112235030.002244067644430.2940732887540.0214363805442-0.0926415742331-0.01245157112730.3625114675870.338012804671-0.483033750645-0.02809263717440.1786280529480.023088780170.0154802229280.1269742891420.01923654356950.11198373170552.708694193655.3900957245289.63470132
22.688179475180.966908443792-1.047635802442.24848426538-0.4479682930681.01272991107-0.01594070030490.06762875683580.2834950786440.0684081950560.1267685820680.2090806371430.0451586240981-0.1536112506530.02684406339790.1212027572960.02274259092470.004691918160110.1059717955090.01977769136890.13600982328256.439969552863.2741833426293.438963241
31.372670801621.307751589770.2655718639381.1574817353-0.5308342909032.17162139911-0.04928480562630.143801202868-0.188738842418-0.05427017482830.1144089979550.2080088641460.241026894004-0.565066240636-0.005878019079760.241782214794-0.02327710239310.008744324245970.2806537851710.0188206701080.1801357895749.312397799550.7390366677290.389098599
42.071416298531.34894726084-0.5790536323981.512668997670.2270505961130.889302184078-0.1308265224770.189457704694-0.181442841904-0.2453567848160.126429811948-0.1444907975290.2905305044440.124143977311-5.79703962965E-70.229462112630.02463081344710.01700308887450.1993605226640.01429212530290.18915624352664.789216649157.2274159245283.235627036
52.273149053511.31564802964-0.8274936939281.86834775146-0.6992368998142.854677739730.0121537662960.2384353245830.400884848270.004432036005370.1169543539130.25928764019-0.3274761286760.09815946490250.0370150466760.1414076087210.00776489381092-0.00225336029370.1383982546460.05258379941730.18420964516873.024998913277.7005561238281.145418845
61.17456971531-0.1918362630340.1467145608980.378469588776-0.5673252991880.9295291934230.0690812877561-0.02894069450291.053037080690.3585524481820.1591329282190.037925709673-0.6535421295060.3011242074850.09325622295770.311992798220.01497007910260.07757596437590.0874878565433-0.0462285484530.44932125993265.84538932878.3424097411291.168928083
71.463709687020.462310855047-0.3779248479921.188054158330.02631143693561.841128341950.1079626457570.0684993524160.2354127375270.01135176537030.0395274056336-0.0947458613694-0.4271969312610.4763515395050.01005307030060.268275985845-0.07427233880440.04709553849380.2315677336460.03378077137460.22009506911981.938579532282.8929507632280.78618401
81.637041306251.62475278416-0.2625743203581.60597404908-0.7850554828051.264045549250.0433032531449-0.1949237565670.00967049527440.0872632949508-0.0558884479916-0.110814352423-0.09070461148630.356737757477-5.26582934861E-70.2075748800080.00793925002932-0.01826832360270.2449031982550.008885082976430.21113609949875.466521335270.3764502446292.610255052
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 11:45)AA11 - 451 - 35
22(chain A and resid 46:105)AA46 - 10536 - 98
33(chain A and resid 106:134)AA106 - 13499 - 127
44(chain A and resid 135:163)AA135 - 163128 - 156
55(chain B and resid 11:84)BE11 - 841 - 77
66(chain B and resid 85:99)BE85 - 9978 - 92
77(chain B and resid 100:132)BE100 - 13293 - 125
88(chain B and resid 133:163)BE133 - 163126 - 156

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