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- PDB-7n13: Crystal structure of MTH1 in complex with compound 32 -

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Basic information

Entry
Database: PDB / ID: 7n13
TitleCrystal structure of MTH1 in complex with compound 32
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE/HYDROLASE inhibitor / Inhibitor / HYDROLASE / 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 / 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 / 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
Chem-ZRV / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsEron, S.J.
CitationJournal: Curr Res Chem Biol / Year: 2021
Title: Development of an AchillesTAG degradation system and its application to control CAR-T activity
Authors: Veits, G.K. / Henderson, C.S. / Vogelaar, A. / Eron, S.J. / Lee, L. / Hart, A. / Deibler, R.W. / Baddour, J. / Elam, W.A. / Agafonov, R.V. / Freda, J. / Chaturvedi, P. / Ladd, B. / Carlson, ...Authors: Veits, G.K. / Henderson, C.S. / Vogelaar, A. / Eron, S.J. / Lee, L. / Hart, A. / Deibler, R.W. / Baddour, J. / Elam, W.A. / Agafonov, R.V. / Freda, J. / Chaturvedi, P. / Ladd, B. / Carlson, M.W. / Vora, H.U. / Scott, T.G. / Tieu, T. / Jain, A. / Chen, C.L. / Kibbler, E.S. / Pop, M.S. / He, M. / Kern, G. / Maple, H.J. / Marsh, G.P. / Norley, M.C. / Oakes, C.S. / Henderson, J.A. / Sowa, M.E. / Phillips, A.J. / Proia, D.A. / Park, E.S. / Patel, J.S. / Fisher, S.L. / Nasveschuk, C.G. / Zeid, R.
History
DepositionMay 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.country / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)37,83710
Polymers36,2312
Non-polymers1,6068
Water5,441302
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8224
Polymers18,1161
Non-polymers7073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0146
Polymers18,1161
Non-polymers8995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.607, 67.835, 79.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth seq-ID: 3 - 155 / Label seq-ID: 5 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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: 18115.590 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-ZRV / 4-anilino-6-[4-(butylcarbamoyl)-3-fluorophenyl]-N-cyclopropyl-7-fluoroquinoline-3-carboxamide


Mass: 514.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H28F2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.21 Å3/Da / Density % sol: 44 % / Description: Long needles
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 23% (w/v) PEG 6k, 200 mM lithium sulfate, 100 mM sodium acetate pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.59→51.48 Å / Num. obs: 43865 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 1.59→1.63 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3200 / CC1/2: 0.587 / Rpim(I) all: 0.918 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ANV

5anv


Resolution: 1.59→51.48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.798 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.254 2194 5.041 %
Rwork0.2116 41329 -
all0.214 --
obs-43523 99.284 %
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: 17.759 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å2-0 Å2
2---0.354 Å20 Å2
3---1.433 Å2
Refinement stepCycle: LAST / Resolution: 1.59→51.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 106 302 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132765
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172543
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6373764
X-RAY DIFFRACTIONr_angle_other_deg1.3271.6155873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3395332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63922.583151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71915468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.91517
X-RAY DIFFRACTIONr_chiral_restr0.0680.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined0.1930.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.22311
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21236
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2204
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.214
X-RAY DIFFRACTIONr_nbd_other0.1490.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.219
X-RAY DIFFRACTIONr_mcbond_it1.6791.6171272
X-RAY DIFFRACTIONr_mcbond_other1.6781.6191273
X-RAY DIFFRACTIONr_mcangle_it2.6292.4261600
X-RAY DIFFRACTIONr_mcangle_other2.6292.4221599
X-RAY DIFFRACTIONr_scbond_it2.6161.9381493
X-RAY DIFFRACTIONr_scbond_other2.5661.8911470
X-RAY DIFFRACTIONr_scangle_it4.0862.7922149
X-RAY DIFFRACTIONr_scangle_other4.0252.7152114
X-RAY DIFFRACTIONr_lrange_it5.98419.0963110
X-RAY DIFFRACTIONr_lrange_other5.87618.5733038
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.054726
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.131230.05008
12BX-RAY DIFFRACTIONLocal ncs0.131230.05008
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
1.59-1.6310.4471690.35229850.35732000.5890.65598.56250.336
1.631-1.6760.3221650.32929000.32931040.7770.7798.74360.31
1.676-1.7240.331390.32528580.32530330.7870.77598.81310.303
1.724-1.7770.3481450.30127570.30429410.7880.82298.67390.272
1.777-1.8350.31500.27326990.27428710.8620.87699.23370.238
1.835-1.90.2731360.2725930.2727610.8730.8698.8410.235
1.9-1.9710.3221310.24925250.25226770.850.89699.21550.223
1.971-2.0520.2861240.22224540.22525900.8950.92299.53670.19
2.052-2.1430.244970.20423710.20624750.9230.93599.71720.175
2.143-2.2470.2581290.2122130.21323620.9070.92899.15330.187
2.247-2.3680.2411110.21421210.21522580.930.92698.84850.183
2.368-2.5120.2641030.19620430.19921500.9250.9499.8140.167
2.512-2.6850.2431010.18819120.1920150.9250.94499.90070.165
2.685-2.8990.2221050.18417770.18618830.930.94399.94690.165
2.899-3.1750.2751070.18216450.18717520.9120.951000.167
3.175-3.5480.177800.17615130.17615950.9620.96299.87460.167
3.548-4.0940.206780.15813320.1614120.9570.9799.85840.153
4.094-5.0060.173580.14611550.14712140.9740.97999.91760.143
5.006-7.0460.281410.29240.2039650.9560.971000.19
7.046-51.4820.195250.2135520.2125790.9670.9699.65460.203

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