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- PDB-6ry4: PARP15 catalytic domain in complex with 4-(3-carbamoylphenoxy)ben... -

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Basic information

Entry
Database: PDB / ID: 6ry4
TitlePARP15 catalytic domain in complex with 4-(3-carbamoylphenoxy)benzamide.
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsPROTEIN BINDING / Inhibitor / Mono-ADP ribosyltransferase..
Function / homology
Function and homology information


NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression ...NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
: / 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. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain ...: / 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. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-(4-aminocarbonylphenoxy)benzamide / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMurthy, S.N. / Maksimainen, M.M. / Lehtio, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Finland
CitationJournal: Chemistryopen / Year: 2021
Title: Evaluation of 3- and 4-Phenoxybenzamides as Selective Inhibitors of the Mono-ADP-Ribosyltransferase PARP10.
Authors: Korn, P. / Classen, A. / Murthy, S. / Guareschi, R. / Maksimainen, M.M. / Lippok, B.E. / Galera-Prat, A. / Sowa, S.T. / Voigt, C. / Rossetti, G. / Lehtio, L. / Bolm, C. / Luscher, B.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.3May 29, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP15
B: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6054
Polymers45,2712
Non-polymers3342
Water4,089227
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-8 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.480, 68.970, 161.250
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 Protein mono-ADP-ribosyltransferase PARP15 / ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly [ADP-ribose] polymerase 15 / PARP-15


Mass: 22635.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP15, BAL3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-KMW / 3-(4-aminocarbonylphenoxy)benzamide


Mass: 256.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NH4Cl pH 7.5, 18% PEG 3350 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 26517 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.051 / Rrim(I) all: 0.12 / Χ2: 0.97 / Net I/σ(I): 10.6
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2756 / Rrim(I) all: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EK2

6ek2


Resolution: 1.95→43.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.399 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21929 1896 5 %RANDOM
Rwork0.18079 ---
obs0.18267 36021 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å2-0 Å2
2---0.43 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 23 227 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133346
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172956
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6674542
X-RAY DIFFRACTIONr_angle_other_deg1.3041.5876889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04322.461191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39215555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3041520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
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_it2.1462.6741586
X-RAY DIFFRACTIONr_mcbond_other2.1462.6731585
X-RAY DIFFRACTIONr_mcangle_it3.4344.0011982
X-RAY DIFFRACTIONr_mcangle_other3.4344.0021983
X-RAY DIFFRACTIONr_scbond_it2.5132.9891760
X-RAY DIFFRACTIONr_scbond_other2.5122.991761
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9714.3682555
X-RAY DIFFRACTIONr_long_range_B_refined6.21531.2343674
X-RAY DIFFRACTIONr_long_range_B_other6.15931.0823642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 137 -
Rwork0.263 2611 -
obs--99.93 %

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