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- PDB-7pwr: PARP15 catalytic domain in complex with OUL254 -

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Basic information

Entry
Database: PDB / ID: 7pwr
TitlePARP15 catalytic domain in complex with OUL254
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / ADP-ribosyltransferase / Inhibitor / Complex
Function / homology
Function and homology information


protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
6-(cyclopentylmethoxy)phthalazine-1,4-dione / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMaksimainen, M.M. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063 and 294085 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Potent 2,3-dihydrophthalazine-1,4-dione derivatives as dual inhibitors for mono-ADP-ribosyltransferases PARP10 and PARP15.
Authors: Nizi, M.G. / Maksimainen, M.M. / Murthy, S. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Sowa, S.T. / Galera-Prat, A. / Prunskaite-Hyyrylainen, R. / Luscher, B. / Korn, P. / Lehtio, L. / Tabarrini, O.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)51,2554
Polymers50,8792
Non-polymers3762
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The dimer formation has been confirmed by Venkannagari et al. https://pubmed.ncbi.nlm.nih.gov/23485441/
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-22 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.370, 69.060, 160.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 25439.459 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 (E. coli)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-89Z / 6-(cyclopentylmethoxy)phthalazine-1,4-dione


Mass: 258.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 67223 / % possible obs: 99.7 % / Redundancy: 4.4 % / CC1/2: 0.995 / Net I/σ(I): 9.99
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 4921 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OTH

7oth


Resolution: 1.6→43.69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.334 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 3362 5 %RANDOM
Rwork0.1462 ---
obs0.1483 63861 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.89 Å2 / Biso mean: 23.534 Å2 / Biso min: 12.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---1.04 Å20 Å2
3---1.93 Å2
Refinement stepCycle: final / Resolution: 1.6→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 27 308 3522
Biso mean--24.52 34.98 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133401
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173124
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.6644628
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5897204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90522.15200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57315569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0571523
X-RAY DIFFRACTIONr_chiral_restr0.0740.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023919
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
X-RAY DIFFRACTIONr_rigid_bond_restr2.04336525
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 246 -
Rwork0.231 4661 -
all-4907 -
obs--99.65 %

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