9QYH | pdb_00009qyh

PARP9 Macro Domain 2 in complex with NAD+

• PDB DOI: https://doi.org/10.2210/pdb9QYH/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 Regional Development Fund, European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.246 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.202 (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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.79 kDa 
• Atom Count: 2,963 
• Modeled Residue Count: 360 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mono-ADP-ribosyltransferase PARP9	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.246 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.428	α = 90
b = 73.827	β = 116.9
c = 58.465	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 Regional Development Fund	European Union	5002550-INSPIRED
European Union (EU)	European Union	101087215-ESPERANCE
European Union (EU)	European Union	101159708-MILESTONE
European Union (EU)	European Union	871037-iNEXT Discovery

Revision History  

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