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- PDB-7pwc: PARP15 catalytic domain in complex with OUL238 -

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Basic information

Entry
Database: PDB / ID: 7pwc
TitlePARP15 catalytic domain in complex with OUL238
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
4-(cyclobutylmethoxy)benzamide / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 6, 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)51,0843
Polymers50,8792
Non-polymers2051
Water4,684260
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 area2070 Å2
ΔGint-9 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.490, 69.200, 162.150
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-8AE / 4-(cyclobutylmethoxy)benzamide


Mass: 205.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / 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: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 82646 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 0.996 / Net I/σ(I): 10.62
Reflection shellResolution: 1.5→1.54 Å / Num. unique obs: 5963 / CC1/2: 0.713

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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: 1.5→43.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.565 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4133 5 %RANDOM
Rwork0.2025 ---
obs0.2035 78513 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.41 Å2 / Biso mean: 19.991 Å2 / Biso min: 9.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0 Å2
2--0.14 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: final / Resolution: 1.5→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 15 261 3453
Biso mean--19.67 28.67 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133317
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173011
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.664506
X-RAY DIFFRACTIONr_angle_other_deg1.3641.5866947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55822.804189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02829
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 298 -
Rwork0.312 5658 -
all-5956 -
obs--98.35 %

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