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- PDB-4gv2: Human ARTD3 (PARP3) - Catalytic domain in complex with inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 4gv2
TitleHuman ARTD3 (PARP3) - Catalytic domain in complex with inhibitor ME0354
ComponentsPoly [ADP-ribose] polymerase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / NAD / ADP-RIBOSE / PARP3 / ARTD3 / ARTD TRANSFERASE DOMAIN / ADP- RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / TRANSFERASE / ADP-RIBOSYLATION
Function / homology
Function and homology information


negative regulation of isotype switching / negative regulation of telomerase RNA reverse transcriptase activity / NAD+- protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation ...negative regulation of isotype switching / negative regulation of telomerase RNA reverse transcriptase activity / NAD+- protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation / intercellular bridge / positive regulation of double-strand break repair via nonhomologous end joining / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / catalytic activity / regulation of mitotic spindle organization / centriole / telomere maintenance / nucleotidyltransferase activity / double-strand break repair / site of double-strand break / nuclear body / centrosome / nucleolus / nucleoplasm / cytoplasm
Similarity search - Function
Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain ...Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical 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. / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5ME / Protein mono-ADP-ribosyltransferase PARP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Lindgren, A.E.G. / Ekblad, T. / Spjut, S. / Andersson, C.D. / Weigelt, J. / Linusson, A. / Elofsson, M. / Schuler, H.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: PARP Inhibitor with Selectivity Toward ADP-Ribosyltransferase ARTD3/PARP3
Authors: Lindgren, A.E.G. / Karlberg, T. / Thorsell, A.G. / Hesse, M. / Spjut, S. / Ekblad, T. / Andersson, C.D. / Pinto, A.F. / Weigelt, J. / Hottiger, M.O. / Linusson, A. / Elofsson, M. / Schuler, H.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1533
Polymers39,7521
Non-polymers4002
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.188, 56.784, 56.618
Angle α, β, γ (deg.)90.00, 112.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly [ADP-ribose] polymerase 3 / PARP-3


Mass: 39752.074 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 178-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-5ME / 3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[(1R)-1-(pyridin-2-yl)ethyl]propanamide


Mass: 322.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N4O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.7M DL-Malic Acid, 0.1M Bis-tris-propane, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2011 / Details: focusing mirrors
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 29876 / Num. obs: 29876 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.106 / Rsym value: 0.091 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2165 / Rsym value: 0.48 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FHB

3fhb


Resolution: 1.8→28.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.882 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19436 1494 5 %RANDOM
Rwork0.16102 ---
all0.16268 28382 --
obs0.16268 28382 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.43 Å2
2---0.71 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 28 178 2958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222842
X-RAY DIFFRACTIONr_bond_other_d0.0010.021915
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.983850
X-RAY DIFFRACTIONr_angle_other_deg0.9123.0014708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75125.313128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6881511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02520
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_it1.0281.51768
X-RAY DIFFRACTIONr_mcbond_other0.2821.5709
X-RAY DIFFRACTIONr_mcangle_it1.82522852
X-RAY DIFFRACTIONr_scbond_it2.74431074
X-RAY DIFFRACTIONr_scangle_it4.5884.5998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 108 -
Rwork0.22 2053 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.885 Å / Origin y: 0.514 Å / Origin z: 11.685 Å
111213212223313233
T0.0159 Å2-0.0008 Å20.0065 Å2-0.0058 Å2-0.0024 Å2--0.0072 Å2
L0.1217 °20.0664 °2-0.0224 °2-0.217 °2-0.0059 °2--0.0996 °2
S-0.0241 Å °-0.0066 Å °-0.0156 Å °-0.0502 Å °0.0144 Å °-0.0256 Å °-0.0119 Å °-0.0017 Å °0.0097 Å °

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