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- PDB-6ek3: PARP15 CATALYTIC DOMAIN MUTANT (Y598L) IN COMPLEX WITH OUL35 -

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Basic information

Entry
Database: PDB / ID: 6ek3
TitlePARP15 CATALYTIC DOMAIN MUTANT (Y598L) IN COMPLEX WITH OUL35
ComponentsPoly [ADP-ribose] polymerase 15
KeywordsTRANSFERASE / Inhibitor / OUL35 / SIGNALING PROTEIN
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
: / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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. ...: / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
4-(4-aminocarbonylphenoxy)benzamide / 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 Finland
Academy of Finland294085 Finland
CitationJournal: Eur J Med Chem / Year: 2018
Title: 4-(Phenoxy) and 4-(benzyloxy)benzamides as potent and selective inhibitors of mono-ADP-ribosyltransferase PARP10/ARTD10.
Authors: Murthy, S. / Desantis, J. / Verheugd, P. / Maksimainen, M.M. / Venkannagari, H. / Massari, S. / Ashok, Y. / Obaji, E. / Nkizinkinko, Y. / Luscher, B. / Tabarrini, O. / Lehtio, L.
History
DepositionSep 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 15
B: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2914
Polymers50,7792
Non-polymers5132
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.200, 68.890, 161.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly [ADP-ribose] polymerase 15 / PARP-15 / ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3


Mass: 25389.443 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 BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q460N3, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-OUL / 4-(4-aminocarbonylphenoxy)benzamide / OUL35


Mass: 256.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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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: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NH4Cl pH 7.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 67204 / % possible obs: 93.7 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rrim(I) all: 0.073 / Net I/σ(I): 13.21
Reflection shellResolution: 1.6→1.64 Å / Mean I/σ(I) obs: 2.09 / Num. unique obs: 4905 / CC1/2: 0.737 / Rrim(I) all: 0.811 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLJ

3blj


Resolution: 1.6→43.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.64 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21029 3361 5 %RANDOM
Rwork0.18343 ---
obs0.18478 63843 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.783 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3---0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.6→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 29 321 3516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193418
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9454655
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25523.793174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91415587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6681523
X-RAY DIFFRACTIONr_chiral_restr0.1040.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212687
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8782.111604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.093.1582010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4692.3951814
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.90329.6235373
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 245 -
Rwork0.262 4653 -
obs--99.82 %

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