9DY4 | pdb_00009dy4

Crystal structure of iron-bound human ADO C18S/C239S variant soaked in hydralazine at 2.39 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb9DY4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-13 Released: 2025-09-24 
• Deposition Author(s): Liu, A., Li, J.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.308 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Hydralazine inhibits cysteamine dioxygenase to treat preeclampsia and senesce glioblastoma

Liu, A., Li, J., Ran, D., Inchul, S.

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: 30.51 kDa 
• Atom Count: 1,870 
• Modeled Residue Count: 232 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-aminoethanethiol dioxygenase	A	274	Homo sapiens	Mutation(s): 2  Gene Names: ADO EC: 1.13.11.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SZ5 (Homo sapiens) Explore Q96SZ5  Go to UniProtKB:  Q96SZ5
PHAROS:  Q96SZ5 GTEx:  ENSG00000181915

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HLZ	C [auth A]	1-hydrazinophthalazine C8 H8 N4 RPTUSVTUFVMDQK-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.308 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.203	α = 90
b = 95.175	β = 90
c = 117.797	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Liu, A., Li, J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-2204225

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release