9HXV | pdb_00009hxv

Crystal structure of TET2-DNA in complex with IOX1

• PDB DOI: https://doi.org/10.2210/pdb9HXV/pdb
• NAKB: 9HXV

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


• Deposited: 2025-01-08 Released: 2025-04-09 
• Deposition Author(s): Niggenaber, J., Mueller, M.P., Rauh, D.
• Funding Organization(s): German Federal Ministry for Education and Research, European Regional Development Fund, Other government, Other private, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.221 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Advancing TET Inhibitor Development: From Structural Insights to Biological Evaluation

Willems, S., Maksumic, L., Niggenaber, J., Lin, T.-C., Schulz, T., Weisner, J., Sievers, S., Mueller, M.-P., Summerer, D., Rauh, D.

(2025) ACS Med Chem Lett 

• DOI: https://doi.org/10.1021/acsmedchemlett.5c00042

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: 59.79 kDa 
• Atom Count: 3,885 
• Modelled Residue Count: 428 
• Deposited Residue Count: 491 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylcytosine dioxygenase TET2	A	467	Homo sapiens	Mutation(s): 0  Gene Names: TET2, KIAA1546, Nbla00191 EC: 1.14.11.80
UniProt & NIH Common Fund Data Resources
Find proteins for Q6N021 (Homo sapiens) Explore Q6N021  Go to UniProtKB:  Q6N021
PHAROS:  Q6N021 GTEx:  ENSG00000168769

Entity ID: 2
Molecule	Chains	Length	Organism	Image
12mer-DNA	B, C	12	Homo sapiens

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8XQ (Subject of Investigation/LOI)	H [auth A]	8-hydroxyquinoline-5-carboxylic acid C10 H7 N O3 JGRPKOGHYBAVMW-UHFFFAOYSA-N
SO4	I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2	D [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.221 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.44	α = 90
b = 89.13	β = 90
c = 268.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Niggenaber, J., Mueller, M.P., Rauh, D.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	01ZX2201B
European Regional Development Fund	European Union	EFRE-800400
Other government		NW21-062C
Other private		Ex-2021-0033
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release