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- PDB-4c9w: Crystal structure of NUDT1 (MTH1) with R-crizotinib -

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Basic information

Entry
Database: PDB / ID: 4c9w
TitleCrystal structure of NUDT1 (MTH1) with R-crizotinib
Components7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
KeywordsHYDROLASE / CRIZOTINIB
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 / 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-VGH / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsElkins, J.M. / Salah, E. / Huber, K. / Superti-Furga, G. / Abdul Azeez, K.R. / Raynor, J. / Krojer, T. / von Delft, F. / Bountra, C. / Edwards, A. / Knapp, S.
CitationJournal: Nature / Year: 2014
Title: Stereospecific Targeting of Mth1 by (S)-Crizotinib as an Anticancer Strategy.
Authors: Huber, K.V.M. / Salah, E. / Radic, B. / Gridling, M. / Elkins, J.M. / Stukalov, A. / Jemth, A. / Gokturk, C. / Sanjiv, K. / Stromberg, K. / Pham, T. / Berglund, U.W. / Colinge, J. / Bennett, ...Authors: Huber, K.V.M. / Salah, E. / Radic, B. / Gridling, M. / Elkins, J.M. / Stukalov, A. / Jemth, A. / Gokturk, C. / Sanjiv, K. / Stromberg, K. / Pham, T. / Berglund, U.W. / Colinge, J. / Bennett, K.L. / Loizou, J.I. / Helleday, T. / Knapp, S. / Superti-Furga, G.
History
DepositionOct 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0668
Polymers18,1001
Non-polymers9667
Water2,810156
1
A: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
hetero molecules

A: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,13116
Polymers36,1992
Non-polymers1,93214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area2050 Å2
ΔGint-126.9 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.200, 59.960, 66.870
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-1157-

CL

21A-1162-

SO4

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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: 18099.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-VGH / 3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine / CRIZOTINIB / Crizotinib


Mass: 450.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22Cl2FN5O / Comment: medication, anticancer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsP36639 ISOFORM 4

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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: 39.63 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2M AMMONIUM SULFATE, 30%(W/V) PEG 4000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→44.64 Å / Num. obs: 18113 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZR0

3zr0


Resolution: 1.65→44.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.329 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21812 923 5.1 %RANDOM
Rwork0.14871 ---
obs0.152 17128 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 51 156 1446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021362
X-RAY DIFFRACTIONr_bond_other_d0.0020.021230
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9951862
X-RAY DIFFRACTIONr_angle_other_deg0.7263.0042841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37924.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67915226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.765157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.691.305631
X-RAY DIFFRACTIONr_mcbond_other1.691.304630
X-RAY DIFFRACTIONr_mcangle_it2.2221.965791
X-RAY DIFFRACTIONr_mcangle_other2.2211.965792
X-RAY DIFFRACTIONr_scbond_it2.2881.68730
X-RAY DIFFRACTIONr_scbond_other2.1081.627711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5242.3261034
X-RAY DIFFRACTIONr_long_range_B_refined3.89612.9811600
X-RAY DIFFRACTIONr_long_range_B_other3.71712.3161538
X-RAY DIFFRACTIONr_rigid_bond_restr2.29432590
X-RAY DIFFRACTIONr_sphericity_free28.595552
X-RAY DIFFRACTIONr_sphericity_bonded8.84752660
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 69 -
Rwork0.184 1193 -
obs--97.53 %

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