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- PDB-5o2d: PARP14 Macrodomain 2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5o2d
TitlePARP14 Macrodomain 2 with inhibitor
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsADP-RIBOSE-BINDING-PROTEIN / PARP / ADP-ribose / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PARP-14, RNA recognition motif 2 / Parp14 WWE domain / : / WWE domain superfamily / WWE domain / WWE domain profile. / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain ...PARP-14, RNA recognition motif 2 / Parp14 WWE domain / : / WWE domain superfamily / WWE domain / WWE domain profile. / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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 / Nucleotide-binding alpha-beta plait domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9HH / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsUth, K. / Schuller, M. / Sieg, C. / Wang, J. / Krojer, T. / Knapp, S. / Riedels, K. / Bracher, F. / Edwards, A.M. / Arrowsmith, C. ...Uth, K. / Schuller, M. / Sieg, C. / Wang, J. / Krojer, T. / Knapp, S. / Riedels, K. / Bracher, F. / Edwards, A.M. / Arrowsmith, C. / Bountra, C. / Elkins, J.M. / Structural Genomics Consortium (SGC)
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Discovery of a Selective Allosteric Inhibitor Targeting Macrodomain 2 of Polyadenosine-Diphosphate-Ribose Polymerase 14.
Authors: Schuller, M. / Riedel, K. / Gibbs-Seymour, I. / Uth, K. / Sieg, C. / Gehring, A.P. / Ahel, I. / Bracher, F. / Kessler, B.M. / Elkins, J.M. / Knapp, S.
History
DepositionMay 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 21, 2018Group: Structure summary / Category: audit_author
Revision 1.3Sep 19, 2018Group: Data collection / Database references / Category: citation_author / diffrn_detector
Item: _citation_author.identifier_ORCID / _diffrn_detector.detector
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9302
Polymers21,5931
Non-polymers3361
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.408, 35.740, 37.150
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1344-

HOH

21A-1421-

HOH

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Components

#1: Protein Poly [ADP-ribose] polymerase 14 / PARP-14 / ADP-ribosyltransferase diphtheria toxin-like 8 / ARTD8 / B aggressive lymphoma protein 2


Mass: 21593.494 Da / Num. of mol.: 1 / Mutation: K1048S,K1154S,K1158S,K1162S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-9HH / ~{N}-[2-(9~{H}-carbazol-1-yl)phenyl]methanesulfonamide


Mass: 336.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N2O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.8M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→27.65 Å / Num. obs: 22712 / % possible obs: 98.9 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1036 / CC1/2: 0.925 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.65 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.135 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17406 1087 4.8 %RANDOM
Rwork0.13003 ---
obs0.13212 21619 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å20.43 Å2
2---0.6 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.6→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 24 130 1590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191564
X-RAY DIFFRACTIONr_bond_other_d0.0020.021462
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9582145
X-RAY DIFFRACTIONr_angle_other_deg0.95633403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72724.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76515268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.88158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
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_it2.111.567789
X-RAY DIFFRACTIONr_mcbond_other2.0451.563788
X-RAY DIFFRACTIONr_mcangle_it2.6412.362995
X-RAY DIFFRACTIONr_mcangle_other2.6442.364996
X-RAY DIFFRACTIONr_scbond_it2.4921.837775
X-RAY DIFFRACTIONr_scbond_other2.4911.837776
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.132.641144
X-RAY DIFFRACTIONr_long_range_B_refined4.69320.131713
X-RAY DIFFRACTIONr_long_range_B_other4.25319.721684
X-RAY DIFFRACTIONr_rigid_bond_restr1.86333026
X-RAY DIFFRACTIONr_sphericity_free29.757578
X-RAY DIFFRACTIONr_sphericity_bonded9.72353038
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 59 -
Rwork0.146 1482 -
obs--91.4 %

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