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- PDB-9rfd: Human ADP-ribosylhydrolase 3 (ARH3) in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 9rfd
TitleHuman ADP-ribosylhydrolase 3 (ARH3) in complex with ADP
ComponentsADP-ribosylhydrolase ARH3
KeywordsHYDROLASE / ADP-ribosylation / ADP-ribosylhydrolase / ARH3
Function / homology
Function and homology information


cellular response to superoxide / peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage ...cellular response to superoxide / peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / POLB-Dependent Long Patch Base Excision Repair / hydrolase activity, hydrolyzing O-glycosyl compounds / base-excision repair, gap-filling / nuclear body / mitochondrial matrix / DNA repair / magnesium ion binding / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / :
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-DIPHOSPHATE / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPaakkonen, J. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland347026 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Discovery and Structural Optimization of 2-Hydrazinopyrimidin-4-one Analogs Inhibiting Human ADP-Ribosylhydrolase ARH3.
Authors: Parviainen, T.A.O. / Duong, M.T.H. / Paakkonen, J. / Burdova, K. / Kuttichova, B. / Hanzlikova, H. / Lehtio, L. / Heiskanen, J.P.
History
DepositionJun 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: 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-ribosylhydrolase ARH3
B: ADP-ribosylhydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,58310
Polymers76,4042
Non-polymers1,1798
Water9,674537
1
A: ADP-ribosylhydrolase ARH3
hetero molecules


  • defined by author
  • Evidence: gel filtration, Single chromatogram peak with retention volume matching the expected for protein monomer, mass spectrometry, Trace amounts of dimer, trimer and tetramer were observed with 5 micromolar sample
  • 38.9 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)38,8696
Polymers38,2021
Non-polymers6685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylhydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7134
Polymers38,2021
Non-polymers5123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.79, 65.76, 69.92
Angle α, β, γ (deg.)116.402, 94.788, 103.731
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ADP-ribosylhydrolase ARH3 / ADP-ribose glycohydrolase ARH3 / ADP-ribosylhydrolase 3 / O-acetyl-ADP-ribose deacetylase ARH3 / ...ADP-ribose glycohydrolase ARH3 / ADP-ribosylhydrolase 3 / O-acetyl-ADP-ribose deacetylase ARH3 / Poly(ADP-ribose) glycohydrolase ARH3 / [Protein ADP-ribosylarginine] hydrolase-like protein 2 / [Protein ADP-ribosylserine] hydrolase


Mass: 38201.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRS, ADPRHL2, ARH3 / Plasmid: pNIC-CFP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NX46, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, poly(ADP-ribose) glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 5 types, 545 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 15% (w/v) PEG 4000, 10% (v/v) DMSO, 0.1 M ammonium sulfate, 0.1 M sodium acetate buffer

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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: Sep 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.85→34.765 Å / Num. obs: 55923 / % possible obs: 96.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.062 / Rrim(I) all: 0.122 / Net I/σ(I): 9.2
Reflection shellResolution: 1.85→1.898 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3577 / CC1/2: 0.816 / CC star: 0.948 / Rpim(I) all: 0.309 / Rrim(I) all: 0.608 / % possible all: 84.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSJun 30, 2024data reduction
XSCALEJun 30, 2024data scaling
PHASERphasing
Coot0.9.8.93model building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→34.765 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.694 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 2000 3.576 %Random selection
Rwork0.1611 53923 --
all0.162 ---
obs0.162 55923 96.691 %-
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: 19.324 Å2
Baniso -1Baniso -2Baniso -3
1--0.122 Å2-0.498 Å2-0.405 Å2
2---0.266 Å20.307 Å2
3---0.273 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 73 537 5722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125321
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164870
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.8267231
X-RAY DIFFRACTIONr_angle_other_deg0.4871.74111224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5035687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.84532
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.00852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58410856
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3110231
X-RAY DIFFRACTIONr_chiral_restr0.0710.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021204
X-RAY DIFFRACTIONr_nbd_refined0.2180.21290
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.24350
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22739
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2407
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2830.238
X-RAY DIFFRACTIONr_nbd_other0.1570.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.240
X-RAY DIFFRACTIONr_mcbond_it1.331.7972730
X-RAY DIFFRACTIONr_mcbond_other1.331.7972728
X-RAY DIFFRACTIONr_mcangle_it2.2033.2143405
X-RAY DIFFRACTIONr_mcangle_other2.2023.2143404
X-RAY DIFFRACTIONr_scbond_it1.8952.0242591
X-RAY DIFFRACTIONr_scbond_other1.8952.0242591
X-RAY DIFFRACTIONr_scangle_it3.1323.6423814
X-RAY DIFFRACTIONr_scangle_other3.1323.6423815
X-RAY DIFFRACTIONr_lrange_it4.93423.3956497
X-RAY DIFFRACTIONr_lrange_other4.80321.3126356
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
1.85-1.8980.291270.23734500.23942450.9610.9784.26380.219
1.898-1.950.2391440.21138800.21242040.9680.97495.71840.192
1.95-2.0060.2551410.1937960.19240330.9590.97897.61960.17
2.006-2.0680.1981360.17936480.17939140.9760.9896.67860.162
2.068-2.1350.2161320.16535680.16738290.9740.98396.6310.151
2.135-2.210.2061280.15334630.15536600.9710.98698.11480.14
2.21-2.2930.1891230.14733110.14935320.9780.98797.22540.134
2.293-2.3860.1931210.14932510.15134590.9780.98797.48480.135
2.386-2.4920.1681150.14731080.14833040.9830.98797.54840.134
2.492-2.6130.1821090.14129490.14331110.980.98898.29640.13
2.613-2.7530.1711060.1428510.14130110.9820.98898.20660.131
2.753-2.9190.2980.14326530.14528020.9750.98798.17990.137
2.919-3.1190.178940.14625260.14826620.980.98798.42220.141
3.119-3.3670.168870.15623350.15624550.9850.98698.65580.153
3.367-3.6840.169810.16321900.16323020.9830.98698.65330.164
3.684-4.1140.179730.14419660.14520650.9810.98898.74090.149
4.114-4.7390.171640.14317280.14418080.9850.98999.1150.151
4.739-5.7770.242540.19214630.19315390.9740.98498.57050.198
5.777-8.060.192430.20811450.20812030.980.9898.75310.216
8.06-34.7650.217240.1866420.1876920.970.98196.24280.213

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