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- PDB-7oqq: PARP15 catalytic domain in complex with TIQ-A -

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Basic information

Entry
Database: PDB / ID: 7oqq
TitlePARP15 catalytic domain in complex with TIQ-A
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 / 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
4H-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: 2 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 4, 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)45,8575
Polymers45,4992
Non-polymers3583
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-5 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.280, 68.540, 159.800
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: 22749.512 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-G18 / 4H-thieno[2,3-c]isoquinolin-5-one


Mass: 201.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H7NOS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 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: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33180 / % possible obs: 96.1 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.05
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.589 / Num. unique obs: 2413 / CC1/2: 0.746

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLJ

3blj


Resolution: 2→42.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.11 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1659 5 %RANDOM
Rwork0.2148 ---
obs0.2169 31520 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.25 Å2 / Biso mean: 27.243 Å2 / Biso min: 13.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å2-0 Å2-0 Å2
2---1.27 Å20 Å2
3---3.73 Å2
Refinement stepCycle: final / Resolution: 2→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 22 97 3307
Biso mean--40.08 26.35 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133350
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173049
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.6674552
X-RAY DIFFRACTIONr_angle_other_deg1.2961.597018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6165405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92422.41195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85715549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3591521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 120 -
Rwork0.328 2294 -
all-2414 -
obs--96.1 %

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