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- PDB-7f43: PARP15 catalytic domain in complex with Niraparib -

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Basic information

Entry
Database: PDB / ID: 7f43
TitlePARP15 catalytic domain in complex with Niraparib
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / Glycosyltransferase / mono-ADP-ribosyltransferase 15
Function / homology
Function and homology information


NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression ...NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
: / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
Chem-3JD / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsZhou, X.L. / Zhou, H. / Li, J. / Zhang, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of the catalytic domain of human PARP15 in complex with small molecule inhibitors
Authors: Zhou, X. / Yang, Y. / Xu, Q. / Zhou, H. / Zhong, F. / Deng, J. / Zhang, J. / Li, J.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 26, 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.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP15
B: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3723
Polymers46,0522
Non-polymers3201
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-10 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.515, 68.726, 160.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP15 / ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly [ADP-ribose] polymerase 15 / PARP-15


Mass: 23025.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP15, BAL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-3JD / 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide / Niraparib


Mass: 320.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES buffer,pH6.5, 22%PEG 3350, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.62→68.73 Å / Num. obs: 746962 / % possible obs: 91.1 % / Redundancy: 12.6 % / Biso Wilson estimate: 18.7599293836 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.8
Reflection shellResolution: 1.62→1.71 Å / Rmerge(I) obs: 0.032 / Num. unique obs: 59161

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLJ

3blj


Resolution: 1.62→63.18 Å / SU ML: 0.235557850029 / Cross valid method: NONE / σ(F): 1.336455182 / Phase error: 33.4056435065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.27544928855 2963 5.07389078206 %
Rwork0.239804486317 55434 -
obs0.24164508022 58397 89.8747229746 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.2932601032 Å2
Refinement stepCycle: LAST / Resolution: 1.62→63.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 24 251 3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006400817067933243
X-RAY DIFFRACTIONf_angle_d0.8397473680494412
X-RAY DIFFRACTIONf_chiral_restr0.0508881301983468
X-RAY DIFFRACTIONf_plane_restr0.00555515176428578
X-RAY DIFFRACTIONf_dihedral_angle_d3.583858240061906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.64730.4005780884041550.331095663332862X-RAY DIFFRACTION98.6270022883
1.6473-1.67570.3576946756381350.3243458059332828X-RAY DIFFRACTION96.6090642321
1.6757-1.70620.3789790526581630.2947932335492792X-RAY DIFFRACTION98.3361064892
1.7062-1.7390.313996279321920.2951867208221976X-RAY DIFFRACTION67.8700361011
1.739-1.77450.3488445493751350.2530769125772874X-RAY DIFFRACTION98.2370225269
1.7745-1.81310.279932051861560.2595984065312836X-RAY DIFFRACTION97.3958333333
1.8131-1.85520.2720542265721480.2683197724452860X-RAY DIFFRACTION98.9148306478
1.8552-1.90160.41244358403410.326475183565790X-RAY DIFFRACTION26.954265326
1.9016-1.95310.4934669060471540.4356524946622686X-RAY DIFFRACTION93.7603169363
1.9531-2.01050.3648605222311450.2934972230512885X-RAY DIFFRACTION97.96314258
2.0105-2.07540.330333398437830.267290731681412X-RAY DIFFRACTION98.0971128609
2.0754-2.14960.3028355493181370.2725620809532889X-RAY DIFFRACTION99.2131147541
2.1496-2.23570.3886705631561490.3043881720262642X-RAY DIFFRACTION90.9120521173
2.2357-2.33740.3976392515091360.3449252304132669X-RAY DIFFRACTION91.6966328866
2.3374-2.46070.2735844039281540.2499606739342924X-RAY DIFFRACTION99.1304347826
2.4607-2.61480.2972272011321590.242048065942910X-RAY DIFFRACTION99.1599353796
2.6148-2.81670.2579794790951700.233899088872944X-RAY DIFFRACTION99.3935525056
2.8167-3.10020.2811730723321480.231282172282935X-RAY DIFFRACTION99.1637182374
3.1002-3.54880.2524762601051820.2041735872472956X-RAY DIFFRACTION99.3352326686
3.5488-4.47090.1954926508161540.1752711730612632X-RAY DIFFRACTION87.6376218937
4.4709-63.180.1742983890471670.1671754377843132X-RAY DIFFRACTION98.272266905

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