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- PDB-7f41: PARP15 catalytic domain in complex with 3-AMINOBENZAMIDE -

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Basic information

Entry
Database: PDB / ID: 7f41
TitlePARP15 catalytic domain in complex with 3-AMINOBENZAMIDE
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / Glycosyltransferase / NAD / 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
: / 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
Similarity search - Domain/homology
3-aminobenzamide / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39721383763 Å
AuthorsZhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of the catalytic domain of human PARP15 in complex with small molecule inhibitors
Authors: Zhou, X. / Yang, Y. / Xu, Q. / Zhou, H. / Zhong, F. / Deng, J. / Zhang, J. / Li, J.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)45,6353
Polymers45,4992
Non-polymers1361
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-11 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.313, 68.498, 158.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 22749.512 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 BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-3AB / 3-aminobenzamide


Mass: 136.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES buffer,pH6.5, 22%PEG 3350, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.39721383763→27.3402061526 Å / Num. obs: 874703 / % possible obs: 85.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 13.1309538906 Å2 / Rsym value: 0.083 / Net I/σ(I): 34.6
Reflection shellResolution: 1.4→1.43 Å / Num. unique obs: 84652 / Rsym value: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLJ

3blj


Resolution: 1.39721383763→27.3402061526 Å / SU ML: 0.137939977293 / Cross valid method: NONE / σ(F): 1.35937084149 / Phase error: 22.1125552579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.217669747105 2000 2.5023772584 %
Rwork0.196396539587 77924 -
obs0.196927035747 79924 81.0810262445 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.1818679805 Å2
Refinement stepCycle: LAST / Resolution: 1.39721383763→27.3402061526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 10 282 3359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005652390627353161
X-RAY DIFFRACTIONf_angle_d0.8632387728934298
X-RAY DIFFRACTIONf_chiral_restr0.0967492162113459
X-RAY DIFFRACTIONf_plane_restr0.0057310930549563
X-RAY DIFFRACTIONf_dihedral_angle_d4.059566597251126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39721383763-1.43220.320956242991750.2574341189792925X-RAY DIFFRACTION43.3087916847
1.4322-1.47090.2533399954771070.2371588282814146X-RAY DIFFRACTION60.8876163207
1.4709-1.51420.25177375071270.2305571894554957X-RAY DIFFRACTION72.878440367
1.5142-1.5630.2547628720091340.2241537239445211X-RAY DIFFRACTION76.9396861955
1.563-1.61890.2416302806571380.2102363165055393X-RAY DIFFRACTION79.3316121629
1.6189-1.68370.2229710333491390.2091512075815415X-RAY DIFFRACTION79.7301177146
1.6837-1.76030.2429339555121400.2101138316495476X-RAY DIFFRACTION80.4238865817
1.7603-1.85310.2223809634681430.2053785370415555X-RAY DIFFRACTION81.4349006717
1.8531-1.96920.2317916629661460.2031218069885683X-RAY DIFFRACTION83.0105383082
1.9692-2.12110.206298250461550.1994419223126040X-RAY DIFFRACTION88.2478632479
2.1211-2.33450.241281034881650.1964201596896407X-RAY DIFFRACTION93.0746353208
2.3345-2.67210.227767866241690.2055786410686611X-RAY DIFFRACTION95.3989024905
2.6721-3.36550.2015824484271770.1963012464656895X-RAY DIFFRACTION98.9644556395
3.3655-27.34020615260.1917965692371850.1715325439197210X-RAY DIFFRACTION99.1286863271

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