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- PDB-9fl6: Human NUDT1 with medetomidine -

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Basic information

Entry
Database: PDB / ID: 9fl6
TitleHuman NUDT1 with medetomidine
ComponentsIsoform p26 of Oxidized purine nucleoside triphosphate hydrolase
KeywordsHYDROLASE / Nudix hydrolase
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 / Phosphate bond hydrolysis by NUDT proteins ...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 / Phosphate bond hydrolysis by NUDT proteins / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
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
: / ACETATE ION / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSalah, E. / Huber, K.V.M. / Elkins, J.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: NUDT1 with medetomidine
Authors: Salah, E. / Huber, K.V.M. / Elkins, J.M.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Isoform p26 of Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3593
Polymers18,1001
Non-polymers2592
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area8220 Å2
Unit cell
Length a, b, c (Å)36.739, 60.850, 67.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Isoform p26 of Oxidized purine nucleoside triphosphate hydrolase / 2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / ...2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / Methylated purine nucleoside triphosphate hydrolase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18099.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NUDT1, Nudix hydrolase 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36639, 2-hydroxy-dATP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-A1IFR / 5-[(1~{R})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole / (R)-4-(1-(2,3-dimethylphenyl)ethyl)-1H-imidazole / Medetomidine


Mass: 200.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 41.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% PEG8000, 0.2 M lithium sulfate and 0.1 M acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.3→67.53 Å / Num. obs: 38033 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.693 / Num. unique obs: 1936 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.205 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.947 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2065 1935 5.097 %
Rwork0.1592 36025 -
all0.161 --
obs-37960 99.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.151 Å2
Baniso -1Baniso -2Baniso -3
1-0.413 Å20 Å2-0 Å2
2---0.492 Å20 Å2
3---0.078 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 19 132 1397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151272
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.6451885
X-RAY DIFFRACTIONr_angle_other_deg1.3111.5972938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3155174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71422.30878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71815232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.251159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_nbd_refined0.2020.2161
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21047
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2574
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2860.29
X-RAY DIFFRACTIONr_nbd_other0.1440.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.213
X-RAY DIFFRACTIONr_mcbond_it1.2541.433653
X-RAY DIFFRACTIONr_mcbond_other1.2411.432651
X-RAY DIFFRACTIONr_mcangle_it1.7512.162824
X-RAY DIFFRACTIONr_mcangle_other1.7552.162825
X-RAY DIFFRACTIONr_scbond_it1.6831.72727
X-RAY DIFFRACTIONr_scbond_other1.6821.72728
X-RAY DIFFRACTIONr_scangle_it2.1842.4791055
X-RAY DIFFRACTIONr_scangle_other2.1842.4791056
X-RAY DIFFRACTIONr_lrange_it2.96817.0021372
X-RAY DIFFRACTIONr_lrange_other2.96717.0071373
X-RAY DIFFRACTIONr_rigid_bond_restr1.11832652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.3-1.3340.2661500.2625800.26127540.8560.85299.12850.249
1.334-1.370.2741290.23525740.23727060.8710.8899.88910.221
1.37-1.410.2391250.2224900.22126170.8880.89799.92360.203
1.41-1.4530.2241310.1824210.18325540.9240.93299.92170.163
1.453-1.5010.1831270.1523460.15224730.9510.9531000.131
1.501-1.5540.2051200.13722840.1424040.9380.9581000.119
1.554-1.6120.1781240.13621860.13923190.9480.96199.61190.118
1.612-1.6780.2081160.13521260.13822420.9450.9591000.118
1.678-1.7520.1741070.12420390.12721480.9640.97199.90690.109
1.752-1.8380.1911030.12619450.1320490.950.96999.95120.115
1.838-1.9370.1641170.12618440.12819610.9650.9751000.115
1.937-2.0540.201880.13917600.14218540.9570.9799.67640.131
2.054-2.1960.158820.14316690.14317510.9730.9711000.137
2.196-2.3710.19980.14615360.14916340.9590.971000.145
2.371-2.5970.18740.15514530.15615270.9640.9641000.155
2.597-2.9020.201830.17912950.18113780.9510.9591000.185
2.902-3.3490.169550.16711840.16712390.9660.9671000.181
3.349-4.0960.219450.14910040.15110500.950.97499.90480.17
4.096-5.7690.266330.1578030.1618360.9550.9751000.189
5.769-45.2050.403280.2494850.2565130.9340.9411000.288

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