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- PDB-4l7u: Human artd3 (parp3) - catalytic domain in complex with inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 4l7u
TitleHuman artd3 (parp3) - catalytic domain in complex with inhibitor ME0398
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 / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / positive regulation of double-strand break repair via nonhomologous end joining / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of telomere maintenance via telomerase ...negative regulation of isotype switching / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / positive regulation of double-strand break repair via nonhomologous end joining / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of telomere maintenance via telomerase / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic activity / NAD+ poly-ADP-ribosyltransferase activity / intercellular bridge / nucleotidyltransferase activity / centriole / telomere maintenance / regulation of mitotic spindle organization / double-strand break repair via nonhomologous end joining / 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-1VC / Protein mono-ADP-ribosyltransferase PARP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: 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 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Data collection / Database references / Derived calculations
Category: reflns_shell / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1312
Polymers39,7521
Non-polymers3791
Water00
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, 56.752, 56.905
Angle α, β, γ (deg.)90.00, 112.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMONOMERIC

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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
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-1VC / methyl N-[3-(4-oxo-3,4-dihydroquinazolin-2-yl)propanoyl]-L-phenylalaninate


Mass: 379.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O4

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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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.9M 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: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 8138 / Num. obs: 8138 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 51.65 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.196 / Net I/σ(I): 9.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 3 / Num. unique obs: 1576 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GV4

4gv4


Resolution: 2.8→27.4 Å / Cor.coef. Fo:Fc: 0.8752 / Cor.coef. Fo:Fc free: 0.7969 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 489 6.01 %RANDOM
Rwork0.2396 ---
all0.2424 8137 --
obs0.2424 8137 99.58 %-
Displacement parametersBiso mean: 42.28 Å2
Baniso -1Baniso -2Baniso -3
1--10.4482 Å20 Å20.5937 Å2
2--9.9435 Å20 Å2
3---0.5047 Å2
Refine analyzeLuzzati coordinate error obs: 0.475 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 28 0 2772
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012835HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.163839HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1306SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes404HARMONIC5
X-RAY DIFFRACTIONt_it2835HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion3.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion358SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3101SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.13 Å
RfactorNum. reflection
Rfree0.3272 -
Rwork0.243 -
all0.243 2307
Refinement TLS params.Method: refined / Origin x: 18.5011 Å / Origin y: 0.3762 Å / Origin z: 11.8757 Å
111213212223313233
T0.1447 Å2-0.0206 Å20.0361 Å2--0.2361 Å2-0.0084 Å2---0.1665 Å2
L0.4916 °2-0.4517 °2-0.2396 °2-2.5371 °20.3366 °2--1.1894 °2
S-0.0148 Å °-0.0306 Å °-0.0179 Å °-0.2945 Å °-0.0485 Å °0.1107 Å °-0.0187 Å °0.0635 Å °0.0633 Å °
Refinement TLS groupSelection details: { A|178 - A|532 }

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