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- PDB-8zv7: PARP15 catalytic domain in complex with RBN012759 -

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Basic information

Entry
Database: PDB / ID: 8zv7
TitlePARP15 catalytic domain in complex with RBN012759
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / Glycosyltransferase / mono-ADP-ribosyltransferase 15
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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / 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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / 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
Chem-XBA / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhou, X.L. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: PARP15 catalytic domain in complex with RBN012759
Authors: Zhou, X.L. / Li, J.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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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)46,2564
Polymers45,4992
Non-polymers7572
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-8 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.753, 49.809, 157.080
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(DE3) (bacteria)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-XBA / 7-(cyclopropylmethoxy)-5-fluoro-2-{[(trans-4-hydroxycyclohexyl)sulfanyl]methyl}quinazolin-4(3H)-one


Mass: 378.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion
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: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→47.84 Å / Num. obs: 331136 / % possible obs: 99.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 30.869461455 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.3
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.449 / Num. unique obs: 31835

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24.88 Å / SU ML: 0.223789686449 / Cross valid method: FREE R-VALUE / σ(F): 1.34756199711 / Phase error: 26.0466603868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239460258194 2003 6.30905883835 %
Rwork0.208532548409 29745 -
obs0.210581002302 31748 99.7016612756 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.486244951 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 52 165 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723268924063258
X-RAY DIFFRACTIONf_angle_d0.8359443552234430
X-RAY DIFFRACTIONf_chiral_restr0.0510151628519469
X-RAY DIFFRACTIONf_plane_restr0.00510757038575571
X-RAY DIFFRACTIONf_dihedral_angle_d4.688261792191906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94320.3035459981861340.262076654392008X-RAY DIFFRACTION96.5299684543
1.9432-1.99570.2898864550791420.2373477143882110X-RAY DIFFRACTION99.9556147359
1.9957-2.05440.2574364411541380.2168185580972074X-RAY DIFFRACTION100
2.0544-2.12070.2729049165111400.2458587118292097X-RAY DIFFRACTION100
2.1207-2.19640.3631138589691430.2409991546692121X-RAY DIFFRACTION100
2.1964-2.28430.30927323761400.2476654496082097X-RAY DIFFRACTION100
2.2843-2.38820.2859253404881460.23442995172123X-RAY DIFFRACTION100
2.3882-2.5140.2618027885941440.2346790596692101X-RAY DIFFRACTION100
2.514-2.67130.2773613170141380.2397941443192107X-RAY DIFFRACTION100
2.6713-2.87730.2738982126341450.2400484034862127X-RAY DIFFRACTION100
2.8773-3.16630.2857374824171480.2321640539022152X-RAY DIFFRACTION100
3.1663-3.62330.2187667989151450.2001823476082153X-RAY DIFFRACTION100
3.6233-4.56040.194990025061460.1692000104062188X-RAY DIFFRACTION99.9571734475
4.5604-24.880.1817735279821540.1799633261632287X-RAY DIFFRACTION99.3487993488

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