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- PDB-8ptt: Human NUDT5 in complex with MRK-952 -

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Basic information

Entry
Database: PDB / ID: 8ptt
TitleHuman NUDT5 in complex with MRK-952
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE / Inhibitor
Function / homology
Function and homology information


ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
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
: / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDiaz-Saez, L. / Koekemoer, L. / Feyerherm, C. / Sloman, S. / Fischer, C. / Schneider, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K.V.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: Human NUDT5 in complex with MRK-952
Authors: Diaz-Saez, L. / Koekemoer, L. / Feyerherm, C. / Sloman, S. / Fischer, C. / Schneider, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K.V.M.
History
DepositionJul 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,34015
Polymers97,4224
Non-polymers1,91811
Water5,224290
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 49.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)49,6828
Polymers48,7112
Non-polymers9716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-82 kcal/mol
Surface area16580 Å2
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


  • defined by author
  • 49.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)49,6587
Polymers48,7112
Non-polymers9475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-72 kcal/mol
Surface area16530 Å2
Unit cell
Length a, b, c (Å)49.245, 59.679, 81.171
Angle α, β, γ (deg.)78.789, 81.715, 76.034
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ADP-sugar pyrophosphatase / 8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked ...8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked moiety X motif 5 / hNUDT5 / YSA1H


Mass: 24355.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, NUDIX5, HSPC115 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 (DE3)
References: UniProt: Q9UKK9, ADP-ribose diphosphatase, 8-oxo-dGDP phosphatase, ADP-D-ribose pyrophosphorylase
#2: Chemical
ChemComp-F2V / 6-[(5~{R})-7-[3-chloranyl-4-(trifluoromethyl)phenyl]-2,7-diazaspiro[4.4]nonan-2-yl]-7-methyl-purine


Mass: 436.861 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H20ClF3N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir: 33% PEG 400, 0.2 M magnesium chloride, and 0.1 M tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.5→28.41 Å / Num. obs: 29822 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.048 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3405 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
REFMAC5.8.0415refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.15 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.815 / ESU R Free: 0.302
RfactorNum. reflection% reflection
Rfree0.2453 1433 4.805 %
Rwork0.178 28389 -
all0.181 --
obs-29822 98.439 %
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: 39.036 Å2
Baniso -1Baniso -2Baniso -3
1-2.431 Å20.788 Å20.886 Å2
2---0.257 Å20.678 Å2
3----1.241 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6062 0 127 290 6479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126433
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166084
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.678786
X-RAY DIFFRACTIONr_angle_other_deg0.2891.57314112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.8045.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43101102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.94110280
X-RAY DIFFRACTIONr_chiral_restr0.2320.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021313
X-RAY DIFFRACTIONr_nbd_refined0.1860.21047
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.25372
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22931
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2307
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.218
X-RAY DIFFRACTIONr_nbd_other0.1650.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.27
X-RAY DIFFRACTIONr_mcbond_it1.6634.0373169
X-RAY DIFFRACTIONr_mcbond_other1.6624.0373169
X-RAY DIFFRACTIONr_mcangle_it2.8567.2483965
X-RAY DIFFRACTIONr_mcangle_other2.8557.2483966
X-RAY DIFFRACTIONr_scbond_it1.6254.243264
X-RAY DIFFRACTIONr_scbond_other1.6254.243265
X-RAY DIFFRACTIONr_scangle_it2.8257.6964810
X-RAY DIFFRACTIONr_scangle_other2.8257.6964811
X-RAY DIFFRACTIONr_lrange_it4.98939.276746
X-RAY DIFFRACTIONr_lrange_other4.96939.2976711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5640.3081110.2442087X-RAY DIFFRACTION98.4767
2.564-2.6340.3451090.2432008X-RAY DIFFRACTION97.7378
2.634-2.710.291060.2531971X-RAY DIFFRACTION97.7872
2.71-2.7920.348980.2271912X-RAY DIFFRACTION98.6261
2.792-2.8830.267820.2181882X-RAY DIFFRACTION98.2491
2.883-2.9830.264960.2081759X-RAY DIFFRACTION97.8892
2.983-3.0950.2961010.2111774X-RAY DIFFRACTION99.1015
3.095-3.2190.268810.2121650X-RAY DIFFRACTION98.6887
3.219-3.360.256830.2031597X-RAY DIFFRACTION98.1882
3.36-3.5220.248830.1831578X-RAY DIFFRACTION98.4588
3.522-3.7090.226640.171438X-RAY DIFFRACTION99.2074
3.709-3.930.247830.171394X-RAY DIFFRACTION98.7299
3.93-4.1960.187580.1371310X-RAY DIFFRACTION99.1304
4.196-4.5240.264510.1421253X-RAY DIFFRACTION99.0881
4.524-4.9430.181600.1341110X-RAY DIFFRACTION99.0686
4.943-5.5060.23400.1441023X-RAY DIFFRACTION98.4259
5.506-6.3180.223340.175908X-RAY DIFFRACTION98.5356
6.318-7.6440.241430.147749X-RAY DIFFRACTION98.0198
7.644-10.440.156290.126609X-RAY DIFFRACTION99.0683
10.44-28.410.183210.183377X-RAY DIFFRACTION99.005

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