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- PDB-4l6z: Human artd3 (parp3) - catalytic domain in complex with inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 4l6z
TitleHuman artd3 (parp3) - catalytic domain in complex with inhibitor STO1168
ComponentsPoly [ADP-ribose] polymerase 3
Keywordstransferase/transferase inhibitor / DIPHTHERIA TOXIN LIKE ADP-RIBOSE TRANSFERASE / TRANSFERASE / ADP-RIBOSYLATION / transferase-transferase inhibitor complex
Function / homology
Function and homology information


negative regulation of isotype switching / : / 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 / : / 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 / positive regulation of double-strand break repair via nonhomologous end joining / intercellular bridge / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic activity / regulation of mitotic spindle organization / telomere maintenance / centriole / 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 / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily ...Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / 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-1DC / Protein mono-ADP-ribosyltransferase PARP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: J.Med.Chem. / Year: 2013
Title: Chemical Probes to Study ADP-Ribosylation: Synthesis and Biochemical Evaluation of Inhibitors of the Human ADP-Ribosyltransferase ARTD3/PARP3.
Authors: Lindgren, A.E. / Karlberg, T. / Ekblad, T. / Spjut, S. / Thorsell, A.G. / Andersson, C.D. / Nhan, T.T. / Hellsten, V. / Weigelt, J. / Linusson, A. / Schuler, H. / Elofsson, M.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

Downloads & links

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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
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.269, 56.804, 56.626
Angle α, β, γ (deg.)90.00, 112.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly [ADP-ribose] polymerase 3 / PARP-3 / hPARP-3 / ADP-ribosyltransferase diphtheria toxin-like 3 / ARTD3 / IRT1 / NAD(+) ADP- ...PARP-3 / hPARP-3 / ADP-ribosyltransferase diphtheria toxin-like 3 / ARTD3 / IRT1 / NAD(+) ADP-ribosyltransferase 3 / ADPRT-3 / Poly[ADP-ribose] synthase 3 / pADPRT-3


Mass: 39752.074 Da / Num. of mol.: 1 / Fragment: CATALYTIC PARP DOMAIN (unp residues 178-532)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRT3, ADPRTL3, PARP3 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 PRARE / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-1DC / 3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[(1S)-1-(pyridin-4-yl)ethyl]propanamide


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


Mass: 18.015 Da / Num. of mol.: 143 / 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: 40.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.7M DL-Malic Acid, 0.1M Bis-tris-propane , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 22044 / Num. obs: 22044 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1622 / Rsym value: 0.48 / % possible all: 98.9

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Processing

Software
NameVersionClassification
GDAdata acqusitiondata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GV4

4gv4


Resolution: 2→28.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.775 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.185 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20953 1103 5 %RANDOM
Rwork0.16154 ---
all0.16393 20941 --
obs0.16393 20941 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: 19.122 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20.32 Å2
2---0.89 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 28 143 2929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222848
X-RAY DIFFRACTIONr_bond_other_d0.0020.021925
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9813857
X-RAY DIFFRACTIONr_angle_other_deg0.9173.0024734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14925.349129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60615491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2841511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
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_it0.931.51768
X-RAY DIFFRACTIONr_mcbond_other0.2271.5709
X-RAY DIFFRACTIONr_mcangle_it1.67822852
X-RAY DIFFRACTIONr_scbond_it2.54431080
X-RAY DIFFRACTIONr_scangle_it4.1364.51005
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 81 -
Rwork0.206 1531 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 18.81 Å / Origin y: 0.515 Å / Origin z: 11.782 Å
111213212223313233
T0.0145 Å20.0007 Å20.007 Å2-0.0046 Å20.0012 Å2--0.0066 Å2
L0.146 °20.0585 °2-0.0221 °2-0.2267 °20.0174 °2--0.1497 °2
S-0.0215 Å °-0.0128 Å °-0.0186 Å °-0.0474 Å °0.0094 Å °-0.0219 Å °-0.0147 Å °0.0012 Å °0.012 Å °

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