9QYF | pdb_00009qyf

PARP9 Macro Domain 2 in complex with ADPr

• PDB DOI: https://doi.org/10.2210/pdb9QYF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-04-17 Released: 2025-05-28 
• Deposition Author(s): Fourkiotis, K.N., Chikunova, A., Tsika, C.A., Kravvariti, P.K., Tsatsouli, A.S., Perrakis, A., Spyroulias, A.G.
• Funding Organization(s): European Union (EU), European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Comparative analysis of hPARP9 macro domains

Fourkiotis, K.N., Chikunova, A., Tsika, C.A., Kravvariti, P.K., Tsatsouli, A.S., Perrakis, A., Spyroulias, A.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.35 kDa 
• Atom Count: 1,863 
• Modeled Residue Count: 190 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mono-ADP-ribosyltransferase PARP9	A	197	Homo sapiens	Mutation(s): 0  Gene Names: PARP9, BAL, BAL1 EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXQ6 (Homo sapiens) Explore Q8IXQ6  Go to UniProtKB:  Q8IXQ6
PHAROS:  Q8IXQ6 GTEx:  ENSG00000138496

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6 (Subject of Investigation/LOI)	C [auth A]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
APR (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.143	α = 90
b = 52.143	β = 90
c = 132.158	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Fourkiotis, K.N., Chikunova, A., Tsika, C.A., Kravvariti, P.K., Tsatsouli, A.S., Perrakis, A., Spyroulias, A.G.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	101087215-ESPERANCE
European Union (EU)	European Union	871037-iNEXT-Discovery
European Regional Development Fund	European Union	5002550-INSPIRED
European Union (EU)	European Union	101159708-MILESTONE

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release