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- PDB-9tcb: Catalytic domain of human PARP15 in complex with BAD -

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Basic information

Entry
Database: PDB / ID: 9tcb
TitleCatalytic domain of human PARP15 in complex with BAD
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / ADP-ribosylation / ADP-ribosyltransferase / ARTD / PARP
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
Chem-DQV / NICOTINAMIDE / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPaakkonen, J. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Biorxiv / Year: 2025
Title: Dimerization of human PARP15 is required for NAD+ binding and automodification
Authors: Tuovinen, A. / Paakkonen, J. / Maksimainen, M.M. / Hirschen, L. / Hentila, H.I. / Tauscher, M. / Luscher, B. / Vela-Rodriguez, C. / Korn, P. / Lehtio, L.
History
DepositionNov 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)46,7204
Polymers45,9362
Non-polymers7852
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-5 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.15, 68.51, 159.61
Angle α, β, γ (deg.)90, 90, 90
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: 22967.785 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 (bacteria)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-DQV / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 662.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG 3350, 0.2 M ammonium chloride No pH buffer in the crystallisation solution; protein stock contained 30 mM Hepes at pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.9→43.483 Å / Num. obs: 39921 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.033 / Rrim(I) all: 0.122 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2916 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.268 / Rrim(I) all: 0.923 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSJun 30, 2023data reduction
XSCALEJun 30, 2023data scaling
PHASER2.8.3phasing
Coot0.9.8.93model building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.483 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.205 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.134 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions and not included in the output file
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1849 4.632 %Random selection
Rwork0.1819 38072 --
all0.184 ---
obs-39921 99.872 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.959 Å2
Baniso -1Baniso -2Baniso -3
1--1.914 Å2-0 Å2-0 Å2
2--0.473 Å2-0 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 53 282 3470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123329
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163004
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.8294538
X-RAY DIFFRACTIONr_angle_other_deg0.511.7746924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6945408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.585520
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.36453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40710532
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.78110160
X-RAY DIFFRACTIONr_chiral_restr0.0690.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
X-RAY DIFFRACTIONr_nbd_refined0.2090.2598
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22744
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21626
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0540.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.221
X-RAY DIFFRACTIONr_nbd_other0.1460.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.216
X-RAY DIFFRACTIONr_mcbond_it2.5983.0591592
X-RAY DIFFRACTIONr_mcbond_other2.5983.061590
X-RAY DIFFRACTIONr_mcangle_it4.085.4881989
X-RAY DIFFRACTIONr_mcangle_other4.0825.4891989
X-RAY DIFFRACTIONr_scbond_it3.083.31737
X-RAY DIFFRACTIONr_scbond_other3.083.31738
X-RAY DIFFRACTIONr_scangle_it4.785.9362541
X-RAY DIFFRACTIONr_scangle_other4.7795.9362542
X-RAY DIFFRACTIONr_lrange_it7.11533.2783830
X-RAY DIFFRACTIONr_lrange_other7.03632.3853765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.3111350.25927770.26129160.9440.95599.86280.24
1.949-2.0020.2561300.23726790.23828110.9590.96399.92880.214
2.002-2.060.2491280.21826350.21927690.9570.96899.78330.193
2.06-2.1240.2681220.20525230.20826520.9520.97299.7360.179
2.124-2.1930.2181200.19624640.19725860.970.97599.92270.175
2.193-2.270.2061180.18324230.18425440.9710.97799.88210.162
2.27-2.3550.2261120.17523230.17824360.9640.9899.9590.157
2.355-2.4510.2451080.18122210.18423310.9640.97899.91420.16
2.451-2.560.2441040.17921470.18222530.9640.9899.91120.161
2.56-2.6840.2391010.17220660.17521670.9690.9821000.157
2.684-2.8290.214960.17819810.17920810.9710.9899.80780.165
2.829-30.204900.1818530.18119440.9730.9899.94860.17
3-3.2060.2850.18417490.18518350.9790.98199.94550.176
3.206-3.4610.25800.19216550.19417360.9640.97999.94240.187
3.461-3.7890.204740.1715230.17215970.9770.9861000.173
3.789-4.2320.195670.1513760.15214430.9760.9871000.158
4.232-4.8790.138600.1412420.1413020.9890.9881000.15
4.879-5.9570.221520.17910590.18111110.9740.9841000.189
5.957-8.3470.247410.2098500.2118910.9750.9781000.222
8.347-43.4830.276260.2185260.2215540.9610.97299.6390.247

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