Skip to main content

 9TCB | pdb_00009tcb

Catalytic domain of human PARP15 in complex with BAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.220 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.191 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9TCB

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Dimerization of human PARP15 is required for NAD + binding and automodification.

Tuovinen, A., Paakkonen, J., Maksimainen, M.M., Hirschen, L., Hentila, H.I., Tauscher, M., Luscher, B., Vela-Rodriguez, C., Korn, P., Lehtio, L.

(2026) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70758
  • Primary Citation Related Structures: 
    9TCB

  • PubMed Abstract: 

    PARP proteins are enzymes catalyzing ADP-ribosylation, a well-conserved post-translational modification. In addition to the catalytic domain present in all PARPs, these proteins have a wide variety of other domains possessing different functions. Additional domains present in human PARP15 are macrodomains, capable of binding ADP-ribose. PARP15 is the least studied of the macrodomain-containing human PARPs, and it is linked to different diseases from infections to cancer. We show that the full-length canonical isoform 1 of PARP15 auto-ADP-ribosylates robustly on glutamate and aspartate residues, from which the modification can be hydrolyzed by known ADP-ribosylhydrolases. We have been able to locate several modification sites in the region of tandem macrodomains. Consistent with previous findings that the catalytic domain dimerization is necessary for enzymatic activity, we confirm this in the full-length context with the recombinant isoform 1 of PARP15. We show that dimerization is required for the efficient substrate NAD + binding, and we provide structural basis for this requirement with the help of a co-crystal structure of the catalytic domain dimer with an unhydrolyzable substrate analog.


  • Organizational Affiliation: 
    • Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.

Macromolecule Content 

  • Total Structure Weight: 46.72 kDa 
  • Atom Count: 3,515 
  • Modeled Residue Count: 394 
  • Deposited Residue Count: 400 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein mono-ADP-ribosyltransferase PARP15
A, B
200Homo sapiensMutation(s): 0 
Gene Names: PARP15, BAL3
EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N3 (Homo sapiens)
Explore Q460N3 
Go to UniProtKB:  Q460N3
PHAROS:  Q460N3
GTEx:  ENSG00000173200 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ460N3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DQV
(Subject of Investigation/LOI)

Query on DQV



Download:Ideal Coordinates CCD File
C [auth A][(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
C22 H28 N6 O14 P2
HNKKJJHKTPALEK-RACQCECLSA-N
NCA
(Subject of Investigation/LOI)

Query on NCA



Download:Ideal Coordinates CCD File
D [auth B]NICOTINAMIDE
C6 H6 N2 O
DFPAKSUCGFBDDF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.220 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.15α = 90
b = 68.51β = 90
c = 159.61γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sigrid Juselius FoundationFinland--
Jane and Aatos Erkko FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-28
    Type: Initial release
  • Version 1.1: 2026-10-14
    Changes: Database references