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- PDB-8hlq: Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain b... -

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Basic information

Entry
Database: PDB / ID: 8hlq
TitleMutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Niraparib (MK-4827)
ComponentsPoly [ADP-ribose] polymerase 2
KeywordsTRANSFERASE / DNA ADP-ribosyltransferase 2 / PARP2 / Niraparib / MK-4827
Function / homology
Function and homology information


response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / NAD+ ADP-ribosyltransferase ...response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA repair-dependent chromatin remodeling / NAD+-protein mono-ADP-ribosyltransferase activity / decidualization / site of DNA damage / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / nucleosome binding / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / base-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. ...: / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
Chem-3JD / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, X.Y. / Zhou, J. / Xu, B.L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82003657 China
National Natural Science Foundation of China (NSFC)81673300 China
National Natural Science Foundation of China (NSFC)82173693 China
CitationJournal: Bioorg.Chem. / Year: 2025
Title: Engaging an engineered PARP-2 catalytic domain mutant to solve the complex structures harboring approved drugs for structure analyses.
Authors: Wang, X. / Zhou, J. / Xu, B.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 2
B: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8497
Polymers79,9322
Non-polymers9175
Water21612
1
A: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3783
Polymers39,9661
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area16510 Å2
MethodPISA
2
B: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4704
Polymers39,9661
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-0 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.431, 88.089, 95.731
Angle α, β, γ (deg.)90.000, 90.490, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Poly [ADP-ribose] polymerase 2 / PARP-2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP- ...PARP-2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP-ribosyltransferase PARP2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2 / Protein poly-ADP-ribosyltransferase PARP2


Mass: 39965.910 Da / Num. of mol.: 2 / Mutation: T349S,L351R,S353G,P354L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-3JD / 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide / Niraparib


Mass: 320.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 25% PEG-3350, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.7→41.43 Å / Num. obs: 19017 / % possible obs: 99.92 % / Redundancy: 5.1 % / Biso Wilson estimate: 58.88 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 15.54
Reflection shellResolution: 2.7→2.796 Å / Num. unique obs: 1891 / CC1/2: 0.853 / CC star: 0.959

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 2.7→41.43 Å / SU ML: 0.3816 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2816 1000 5.26 %
Rwork0.226 18017 -
obs0.2291 19017 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.59 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 66 12 5682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045845
X-RAY DIFFRACTIONf_angle_d0.59117891
X-RAY DIFFRACTIONf_chiral_restr0.0382848
X-RAY DIFFRACTIONf_plane_restr0.00571014
X-RAY DIFFRACTIONf_dihedral_angle_d20.93782206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.38751240.30652578X-RAY DIFFRACTION99.89
2.84-3.020.35181310.29212577X-RAY DIFFRACTION99.96
3.02-3.250.32391670.29362545X-RAY DIFFRACTION100
3.25-3.580.36461190.26912563X-RAY DIFFRACTION99.89
3.58-4.10.30791610.22272558X-RAY DIFFRACTION99.93
4.1-5.160.23651340.19322596X-RAY DIFFRACTION100
5.16-41.430.21671640.18332600X-RAY DIFFRACTION99.93

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