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- PDB-9rfe: Human ADP-ribosylhydrolase 3 (ARH3) in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 9rfe
TitleHuman ADP-ribosylhydrolase 3 (ARH3) in complex with an inhibitor
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 / 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

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Assembly

Deposited unit
A: ADP-ribosylhydrolase ARH3
B: ADP-ribosylhydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0878
Polymers76,4042
Non-polymers6836
Water6,125340
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
  • 38.5 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)38,5434
Polymers38,2021
Non-polymers3423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylhydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5434
Polymers38,2021
Non-polymers3423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.22, 66.02, 70.86
Angle α, β, γ (deg.)115.28, 96.392, 104.332
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-A1JFJ / 2-[(2~{E})-2-[1-(4-aminophenyl)ethylidene]hydrazinyl]-6-methyl-1~{H}-pyrimidin-4-one


Mass: 257.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 10% (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 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.85→35.995 Å / Num. obs: 57348 / % possible obs: 96.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Net I/σ(I): 14.4
Reflection shellResolution: 1.85→1.898 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3730 / CC1/2: 0.869 / CC star: 0.964 / Rpim(I) all: 0.257 / Rrim(I) all: 0.504 / % possible all: 84.7

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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→35.995 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.891 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 2000 3.487 %Random selection
Rwork0.1627 55348 --
all0.164 ---
obs-57348 96.58 %-
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: 34.951 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.544 Å2-0.808 Å2
2---0.481 Å20.909 Å2
3---0.267 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5051 0 48 340 5439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125229
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164714
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.8187112
X-RAY DIFFRACTIONr_angle_other_deg0.4981.72810853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.9567.2540
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg3.154206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89910800
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.04110224
X-RAY DIFFRACTIONr_chiral_restr0.0730.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021202
X-RAY DIFFRACTIONr_nbd_refined0.220.21312
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.24307
X-RAY DIFFRACTIONr_nbtor_refined0.180.22737
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2870.229
X-RAY DIFFRACTIONr_nbd_other0.1480.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.227
X-RAY DIFFRACTIONr_mcbond_it1.42.0192730
X-RAY DIFFRACTIONr_mcbond_other1.3812.0192729
X-RAY DIFFRACTIONr_mcangle_it2.1433.623407
X-RAY DIFFRACTIONr_mcangle_other2.1433.6183406
X-RAY DIFFRACTIONr_scbond_it2.0682.2582499
X-RAY DIFFRACTIONr_scbond_other2.0672.2592500
X-RAY DIFFRACTIONr_scangle_it3.3574.0973695
X-RAY DIFFRACTIONr_scangle_other3.3564.0983696
X-RAY DIFFRACTIONr_lrange_it5.54924.7736300
X-RAY DIFFRACTIONr_lrange_other5.50822.7876236
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
1.85-1.8980.2381300.22736000.22844030.9590.96484.7150.205
1.898-1.950.2521420.20939550.21142570.9570.96896.24150.186
1.95-2.0060.2051410.18938910.1941560.9730.97797.01640.166
2.006-2.0680.2221360.17737620.17940290.9690.97996.74860.156
2.068-2.1350.1971330.16436670.16539190.9750.98396.96350.145
2.135-2.210.1981280.15335550.15437840.9780.98597.33090.136
2.21-2.2930.1871230.15234040.15336200.9780.98597.43090.139
2.293-2.3860.1841210.15233340.15335370.9780.98697.68170.137
2.386-2.4920.21140.15331690.15533640.9760.98697.59210.141
2.492-2.6130.1931100.15930510.1632330.9780.98597.7730.149
2.613-2.7530.1961040.1528780.15130430.9790.98797.99540.143
2.753-2.9190.1951000.1527560.15129060.9780.98698.27940.145
2.919-3.1190.185930.15325890.15427230.9770.98598.49430.153
3.119-3.3670.202880.16224340.16325550.9730.98598.70840.167
3.367-3.6850.232810.17422280.17623390.9730.98498.71740.184
3.685-4.1150.18730.13820240.1421230.9820.98998.77530.154
4.115-4.7410.165640.13417660.13618560.9850.9998.59910.155
4.741-5.7820.213550.17815180.17915920.9750.98498.80650.206
5.782-8.0730.214420.20311660.20312330.9790.97897.97240.236
8.073-35.9950.292220.1976010.27010.8990.97388.8730.243
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.73330.01990.85051.76810.36633.65040.07060.17580.07010.0680.0548-0.24490.2910.1355-0.12540.02410.0121-0.01520.0199-0.00160.0415-7.0966-11.34179.9034
22.10220.25910.72652.36740.7772.3761-0.1643-0.2283-0.0697-0.01510.04290.1588-0.2291-0.11040.12140.03770.024-0.00140.02850.01020.019313.8498-39.540732.7622
Refinement TLS groupSelection: ALL

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