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- PDB-7oux: PARP15 catalytic domain in complex with OUL228 -

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Basic information

Entry
Database: PDB / ID: 7oux
TitlePARP15 catalytic domain in complex with OUL228
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / Inhibitor / Complex / ADP-ribosyl-transferase
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 / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / NAD+ 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. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
8-ethoxy-4~{H}-thieno[2,3-c]isoquinolin-5-one / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMaksimainen, M.M. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063 Finland
Academy of Finland294085 Finland
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs.
Authors: Maksimainen, M.M. / Murthy, S. / Sowa, S.T. / Galera-Prat, A. / Rolina, E. / Heiskanen, J.P. / Lehtio, L.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: 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)51,2024
Polymers50,8792
Non-polymers3232
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The dimer formation in a solution has been confirmed by Venkannagari et al. Eur J Pharm Sci . 2013 May 13;49(2):148-56.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-6 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.170, 68.580, 159.260
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-1O7 / 8-ethoxy-4~{H}-thieno[2,3-c]isoquinolin-5-one


Mass: 245.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium chloride pH 7.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 36962 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.998 / Net I/σ(I): 11.71
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2657 / CC1/2: 0.818

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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: 3BLJ

3blj


Resolution: 1.95→43.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.863 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1849 5 %RANDOM
Rwork0.1801 ---
obs0.1819 35113 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.2 Å2 / Biso mean: 34.101 Å2 / Biso min: 20.63 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å2-0 Å2-0 Å2
2--0.18 Å2-0 Å2
3---2.38 Å2
Refinement stepCycle: final / Resolution: 1.95→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 21 171 3385
Biso mean--38.33 37.99 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133331
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173024
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.6594524
X-RAY DIFFRACTIONr_angle_other_deg1.3031.5866965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8625401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22622.593189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69915544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1681519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02834
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 133 -
Rwork0.271 2522 -
all-2655 -
obs--99.96 %

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