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- PDB-4pjv: Structure of PARP2 catalytic domain bound to inhibitor BMN 673 -

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Basic information

Entry
Database: PDB / ID: 4pjv
TitleStructure of PARP2 catalytic domain bound to inhibitor BMN 673
ComponentsPoly [ADP-ribose] polymerase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PARP2 / Inhibitor / Complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding ...hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / DNA repair-dependent chromatin remodeling / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / extrinsic apoptotic signaling pathway / nucleosome binding / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus
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-2YQ / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAoyagi-Scharber, M. / Gardberg, A.S. / Edwards, T.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structural basis for the inhibition of poly(ADP-ribose) polymerases 1 and 2 by BMN 673, a potent inhibitor derived from dihydropyridophthalazinone.
Authors: Aoyagi-Scharber, M. / Gardberg, A.S. / Yip, B.K. / Wang, B. / Shen, Y. / Fitzpatrick, P.A.
History
DepositionMay 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_keywords / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 2
B: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6937
Polymers83,6562
Non-polymers1,0375
Water2,576143
1
A: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3924
Polymers41,8281
Non-polymers5653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3003
Polymers41,8281
Non-polymers4722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.860, 57.740, 69.290
Angle α, β, γ (deg.)77.28, 79.99, 63.88
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 234 - 579 / Label seq-ID: 23 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Poly [ADP-ribose] polymerase 2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 ...hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2


Mass: 41827.922 Da / Num. of mol.: 2
Fragment: PARP2 HELICAL AND CATALYTIC DOMAINS (UNP residues 235-579)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): NEB T7 EXPRESS / References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-2YQ / (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one / Talazoparib


Mass: 380.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14F2N6O / Comment: medication, anticancer, inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPRO to HIS conflict in unp entry Q9UGN5

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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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: (W/V) POLYETHYLENE GLYCOL 3350, 333 mM SODIUM CHLORIDE.
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.097 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.097 Å / Relative weight: 1
ReflectionResolution: 2.5→67.33 Å / Num. obs: 22773 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 25.67 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.02
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.8 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KCZ

3kcz


Resolution: 2.5→67.33 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.848 / SU B: 22.703 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.366 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1150 5 %RANDOM
Rwork0.214 ---
obs0.218 22773 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0.62 Å20.07 Å2
2--0.43 Å20.35 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 2.5→67.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 74 143 5331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025299
X-RAY DIFFRACTIONr_bond_other_d0.0010.023474
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9847185
X-RAY DIFFRACTIONr_angle_other_deg0.93138503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75324.338219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39115864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2221522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215887
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021039
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4213 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.30.5
medium thermal3.262
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 70 -
Rwork0.288 1614 -
obs--91.47 %
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)
10.6812-1.3619-0.03913.0606-0.31631.6274-0.0429-0.0917-0.14250.29950.09910.2494-0.233-0.1533-0.05620.141-0.0507-0.00640.1668-0.00780.09689.4267.103-5.053
20.3321-0.7469-0.43654.14150.88830.79340.1356-0.0331-0.01720.0874-0.154-0.1368-0.1215-0.01410.01840.1565-0.0128-0.04630.18130.00490.055410.44610.806-6.62
31.6306-0.1729-0.131.3293-0.46091.8185-0.0246-0.05080.0046-0.05550.0029-0.06860.09490.07210.02170.11270.02220.01320.0788-0.01920.010728.611-2.812-5.016
42.4469-3.03941.04883.8176-1.27911.4417-0.01090.10080.37770.0474-0.0131-0.4773-0.1563-0.06430.0240.299-0.0465-0.04360.26610.03960.12296.43933.752-41.129
52.5469-2.6141.0362.9159-1.15791.01220.0365-0.0926-0.11670.1760.0510.0749-0.325-0.0282-0.08750.3047-0.0174-0.01340.19180.00540.02192.26935.06-39.089
61.1978-0.1803-0.06561.509-0.20133.0658-0.0404-0.01170.0432-0.07370.04140.01140.17130.0226-0.00110.09250.04980.00270.04930.00270.00213.96312.413-40.364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A234 - 292
2X-RAY DIFFRACTION2A296 - 369
3X-RAY DIFFRACTION3A370 - 579
4X-RAY DIFFRACTION4B234 - 289
5X-RAY DIFFRACTION5B296 - 369
6X-RAY DIFFRACTION6B370 - 579

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