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- PDB-4l7p: Human artd3 (parp3) - catalytic domain in complex with inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 4l7p
TitleHuman artd3 (parp3) - catalytic domain in complex with inhibitor ME0395
ComponentsPoly [ADP-ribose] polymerase 3
Keywordstransferase/transferase inhibitor / DIPHTHERIA TOXIN LIKE ADP-RIBOSE TRASNFERASE / TRANSFERASE / ADP-RIBOSYLATION / transferase-transferase inhibitor complex
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 / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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-M95 / Protein mono-ADP-ribosyltransferase PARP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,1012
Polymers39,7521
Non-polymers3491
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.876, 56.535, 58.622
Angle α, β, γ (deg.)90.00, 114.26, 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-M95 / (2E)-N-[(2S)-1-hydroxy-3-phenylpropan-2-yl]-3-(4-oxo-1,4-dihydroquinazolin-2-yl)prop-2-enamide


Mass: 349.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
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: 2.3→30 Å / Num. all: 15221 / Num. obs: 15221 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 40.27 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.106 / Net I/σ(I): 19.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1133 / Rsym value: 0.523 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GV4

4gv4


Resolution: 2.3→20.76 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1216 8 %RANDOM
Rwork0.1833 ---
all0.1874 15206 --
obs0.1874 15206 99.88 %-
Displacement parametersBiso mean: 42.57 Å2
Baniso -1Baniso -2Baniso -3
1--4.327 Å20 Å24.3331 Å2
2--9.0731 Å20 Å2
3----4.7462 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 2.3→20.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 26 46 2795
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012810HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063807HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1297SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes403HARMONIC5
X-RAY DIFFRACTIONt_it2810HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion2.84
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_contact3065SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.46 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2291 220 8.01 %
Rwork0.1829 2525 -
all0.1867 2745 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: 2.222 Å / Origin y: -0.5828 Å / Origin z: 22.849 Å
111213212223313233
T-0.0873 Å2-0.0187 Å20.0149 Å2--0.0978 Å2-0.0035 Å2---0.0374 Å2
L0.6632 °2-0.179 °20.0976 °2-1.1064 °2-0.3052 °2--1.0443 °2
S0.0452 Å °-0.0825 Å °-0.0143 Å °0.1086 Å °0.0188 Å °0.1345 Å °-0.0072 Å °-0.033 Å °-0.064 Å °
Refinement TLS groupSelection details: { A|177 - A|532 }

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