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- PDB-6i8m: THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 6i8m
TitleTHE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH ISOINDOLINONE INHIBITOR
ComponentsPoly [ADP-ribose] polymerase 1
KeywordsTRANSFERASE / CHICKEN PARP1 / INHIBITOR COMPLEX / ADP-RIBOSYLATION / DNA DAMAGE
Function / homology
Function and homology information


NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / replication fork reversal / ATP generation from poly-ADP-D-ribose / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation ...NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / replication fork reversal / ATP generation from poly-ADP-D-ribose / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / positive regulation of double-strand break repair via homologous recombination / protein poly-ADP-ribosylation / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / negative regulation of innate immune response / nucleotidyltransferase activity / NAD binding / double-strand break repair / site of double-strand break / damaged DNA binding / innate immune response / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / cytosol
Similarity search - Function
: / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily ...: / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / 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 / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-H7W / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsCasale, E. / Papeo, G. / Montagnoli, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Discovery of Stereospecific PARP-1 Inhibitor Isoindolinone NMS-P515.
Authors: Papeo, G. / Orsini, P. / Avanzi, N.R. / Borghi, D. / Casale, E. / Ciomei, M. / Cirla, A. / Desperati, V. / Donati, D. / Felder, E.R. / Galvani, A. / Guanci, M. / Isacchi, A. / Posteri, H. / ...Authors: Papeo, G. / Orsini, P. / Avanzi, N.R. / Borghi, D. / Casale, E. / Ciomei, M. / Cirla, A. / Desperati, V. / Donati, D. / Felder, E.R. / Galvani, A. / Guanci, M. / Isacchi, A. / Posteri, H. / Rainoldi, S. / Riccardi-Sirtori, F. / Scolaro, A. / Montagnoli, A.
History
DepositionNov 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9832
Polymers40,6281
Non-polymers3551
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.053, 64.299, 97.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 40627.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residue G652 and P653 are expression tag / Source: (gene. exp.) Gallus gallus (chicken) / Gene: PARP1, ADPRT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26446, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-H7W / (1~{S})-2-(1-cyclohexylpiperidin-4-yl)-1-methyl-3-oxidanylidene-1~{H}-isoindole-4-carboxamide


Mass: 355.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.33 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20-25% PEG 550, 8% 2-propanol and 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.961 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 21543 / % possible obs: 97.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.8 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 2.1→32.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.952 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26012 1099 5.1 %RANDOM
Rwork0.20716 ---
obs0.20985 20403 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.806 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å2-0 Å2-0 Å2
2--2.26 Å2-0 Å2
3----4.05 Å2
Refinement stepCycle: 1 / Resolution: 2.1→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 26 41 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.6483776
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2435347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.93324.496129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40615492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.373159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022069
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.4364.8011391
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.997.1781737
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5425.0461395
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.10464.3834003
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.41 66 -
Rwork0.282 1350 -
obs--88.94 %

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