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- PDB-3c4h: Human poly(ADP-ribose) polymerase 3, catalytic fragment in comple... -

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Basic information

Entry
Database: PDB / ID: 3c4h
TitleHuman poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor DR2313
ComponentsPoly(ADP-ribose) polymerase 3
KeywordsTRANSFERASE / enzyme-inhibitor complex / catalytic fragment / Structural Genomics / Structural Genomics Consortium / SGC / Glycosyltransferase / NAD / Nucleus
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-DRL / Protein mono-ADP-ribosyltransferase PARP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLehtio, L. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Lehtio, L. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Welin, M. / Weigelt, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3.
Authors: Lehtio, L. / Jemth, A.S. / Collins, R. / Loseva, O. / Johansson, A. / Markova, N. / Hammarstrom, M. / Flores, A. / Holmberg-Schiavone, L. / Weigelt, J. / Helleday, T. / Schuler, H. / Karlberg, T.
History
DepositionJan 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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)40,0123
Polymers39,7521
Non-polymers2602
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 57.330, 56.260
Angle α, β, γ (deg.)90.00, 112.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(ADP-ribose) polymerase 3 / PARP-3 / NAD(+) ADP-ribosyltransferase 3 / Poly[ADP-ribose] synthetase 3 / pADPRT-3 / hPARP-3 / IRT1


Mass: 39752.074 Da / Num. of mol.: 1 / Fragment: Catalytic fragment: Residues 178-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP3, ADPRT3, ADPRTL3 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-DRL / 2-methyl-3,5,7,8-tetrahydro-4H-thiopyrano[4,3-d]pyrimidin-4-one


Mass: 182.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2OS
#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.: 153 / 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: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9 M DL-Malic acid, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 18978 / Num. obs: 18978 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.22
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.64 / Num. unique all: 2442 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PA9

2pa9
PDB Unreleased entry


Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.747 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24197 949 5 %RANDOM
Rwork0.17421 ---
all0.17758 18027 --
obs0.17758 18027 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.15 Å2
2---0.19 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 16 153 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9763896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.98925.156128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78215494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.771511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022188
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21177
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21925
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5681.51851
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94122897
X-RAY DIFFRACTIONr_scbond_it1.39731141
X-RAY DIFFRACTIONr_scangle_it2.2014.5996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 67 -
Rwork0.197 1269 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3938-0.8962-0.12342.0108-0.27080.9238-0.1029-0.0659-0.0930.0855-0.003-0.22130.08560.28080.106-0.1047-0.0015-0.00390.0053-0.0004-0.05630.1572.393521.9028
21.0170.60730.24344.38921.72791.42260.00910.06670.0338-0.2806-0.0196-0.099-0.2075-0.01950.0105-0.05510.0325-0.0279-0.02170.0441-0.10110.963710.55828.2466
31.48140.3083-0.0692.37720.14681.2254-0.0405-0.0053-0.059-0.10440.0269-0.03360.0352-0.02530.0136-0.0776-0.0071-0.0034-0.04180.0031-0.09613.7727-6.79385.5697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA176 - 2981 - 123
2X-RAY DIFFRACTION2AA299 - 376124 - 201
3X-RAY DIFFRACTION3AA377 - 532202 - 357

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