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- PDB-6aa5: Crystal structure of MTH1 in complex with 3-isomangostin -

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Basic information

Entry
Database: PDB / ID: 6aa5
TitleCrystal structure of MTH1 in complex with 3-isomangostin
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsANTITUMOR PROTEIN / HYDROLASE / NUDT1
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 / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-MKU / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsYokoyama, T. / Kitakami, R. / Mizuguchi, M.
CitationJournal: Eur J Med Chem / Year: 2019
Title: Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening.
Authors: Yokoyama, T. / Kitakami, R. / Mizuguchi, M.
History
DepositionJul 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,6886
Polymers18,9861
Non-polymers7035
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-61 kcal/mol
Surface area8440 Å2
2
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)39,37712
Polymers37,9712
Non-polymers1,40510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area2460 Å2
ΔGint-205 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.086, 67.086, 141.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein 7,8-dihydro-8-oxoguanine triphosphatase


Mass: 18985.562 Da / Num. of mol.: 1 / Fragment: UNP residues 44-197
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-MKU / 5,9-dihydroxy-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H,6H-pyrano[3,2-b]xanthen-6-one / 3-isomangostin


Mass: 410.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 41.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 1.8 mM ZnSO4, 6% sucrose, 0.1 M Bis-Tris pH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→39.4 Å / Num. obs: 13042 / % possible obs: 99.5 % / Redundancy: 9.3 % / Rpim(I) all: 0.023 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 1276 / Rpim(I) all: 0.303

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1069: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AA3

6aa3


Resolution: 1.901→38.496 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.96
RfactorNum. reflection% reflection
Rfree0.2384 652 5.01 %
Rwork0.1908 --
obs0.1932 13026 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→38.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1324 0 38 118 1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061411
X-RAY DIFFRACTIONf_angle_d0.9271906
X-RAY DIFFRACTIONf_dihedral_angle_d18.939529
X-RAY DIFFRACTIONf_chiral_restr0.083192
X-RAY DIFFRACTIONf_plane_restr0.006245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9014-2.04820.28721270.21292420X-RAY DIFFRACTION100
2.0482-2.25430.27361260.2352382X-RAY DIFFRACTION98
2.2543-2.58050.23971300.19872466X-RAY DIFFRACTION100
2.5805-3.25090.22561310.20012489X-RAY DIFFRACTION100
3.2509-38.5040.22841380.17132617X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.2651 Å / Origin y: -15.4131 Å / Origin z: 17.4892 Å
111213212223313233
T0.1421 Å20.0174 Å20.0125 Å2-0.1695 Å20.0029 Å2--0.1953 Å2
L1.3045 °2-0.5944 °2-0.4129 °2-1.7051 °20.9264 °2--3.9463 °2
S0.0025 Å °-0.0072 Å °0.061 Å °-0.0757 Å °0.086 Å °0.0168 Å °0.0244 Å °0.1562 Å °0.084 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 3:164 )

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