9QYD | pdb_00009qyd

PARP9 Macro domain 1, Free form

• PDB DOI: https://doi.org/10.2210/pdb9QYD/pdb

• Classification: HYDROLASE
• 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, N.K., Chikunova, A., Tsika, C.A., Tsatsouli, A.S., Perrakis, A., Spyroulias, G.A.
• Funding Organization(s): European Regional Development Fund, European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.235 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: in silico

Literature

Comparative analysis of hPARP9 macro domains

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

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: 22.39 kDa 
• Atom Count: 1,623 
• Modeled Residue Count: 195 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mono-ADP-ribosyltransferase PARP9	A	203	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
MLI	C [auth A], D [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	B [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.235 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.701	α = 90
b = 63.847	β = 90
c = 69.53	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, N.K., Chikunova, A., Tsika, C.A., Tsatsouli, A.S., Perrakis, A., Spyroulias, G.A.

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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	101159708-iNEXT Discovery

Revision History  

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