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- PDB-7z1y: PARP15 catalytic domain in complex with OUL245 -

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Basic information

Entry
Database: PDB / ID: 7z1y
TitlePARP15 catalytic domain in complex with OUL245
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / PARP / Inhibitor / Complex
Function / homology
Function and homology information


NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity ...NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 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 / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
[1,2,4]triazolo[3,4-b][1,3]benzothiazol-6-ol / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMaksimainen, M.M. / Lehtio, L.
Funding support Finland, 3items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
Academy of Finland287063 Finland
Academy of Finland294085 Finland
CitationJournal: J.Med.Chem. / Year: 2023
Title: [1,2,4]Triazolo[3,4- b ]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes.
Authors: Murthy, S. / Nizi, M.G. / Maksimainen, M.M. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Vagaggini, C. / Sowa, S.T. / Galera-Prat, A. / Ashok, Y. / Venkannagari, H. / Prunskaite- ...Authors: Murthy, S. / Nizi, M.G. / Maksimainen, M.M. / Massari, S. / Alaviuhkola, J. / Lippok, B.E. / Vagaggini, C. / Sowa, S.T. / Galera-Prat, A. / Ashok, Y. / Venkannagari, H. / Prunskaite-Hyyrylainen, R. / Dreassi, E. / Luscher, B. / Korn, P. / Tabarrini, O. / Lehtio, L.
History
DepositionFeb 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 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)51,1484
Polymers50,8792
Non-polymers2692
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-6 kcal/mol
Surface area18920 Å2
Unit cell
Length a, b, c (Å)45.230, 68.330, 158.650
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-I5F / [1,2,4]triazolo[3,4-b][1,3]benzothiazol-6-ol


Mass: 191.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5N3OS / 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.: 121 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride pH 7.5, 16-20% 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 EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 50369 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 3652 / CC1/2: 0.747

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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: 1.75→43.53 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.495 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 2519 5 %RANDOM
Rwork0.226 ---
obs0.2278 47849 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: 84.41 Å2 / Biso mean: 26.196 Å2 / Biso min: 13.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-0 Å2-0 Å2
2---1.25 Å20 Å2
3---3.58 Å2
Refinement stepCycle: final / Resolution: 1.75→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 17 121 3328
Biso mean--47.44 29.76 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133309
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153001
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6594490
X-RAY DIFFRACTIONr_angle_other_deg1.3061.5876911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69222.804189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70615542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2481518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 183 -
Rwork0.374 3467 -
all-3650 -
obs--99.18 %

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