9VG4 | pdb_00009vg4

Structural complex of FTO bound with 8j

• PDB DOI: https://doi.org/10.2210/pdb9VG4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-06-12 Released: 2025-11-05 
• Deposition Author(s): Yang, C.-G., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.252 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structural complex of FTO bound with 8j

Yang, C.-G., Gan, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.3 kDa 
• Atom Count: 3,392 
• Modeled Residue Count: 432 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase FTO	A	475	Homo sapiens	Mutation(s): 0  Gene Names: FTO, KIAA1752 EC: 1.14.11 (PDB Primary Data), 1.14.11.53 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0B1 (Homo sapiens) Explore Q9C0B1  Go to UniProtKB:  Q9C0B1
PHAROS:  Q9C0B1 GTEx:  ENSG00000140718

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ER2 (Subject of Investigation/LOI)	B [auth A]	2-[[2-chloranyl-6-ethyl-4-[2-[[(E)-4-oxidanyl-4-oxidanylidene-but-2-enoyl]amino]ethylcarbamoyl]phenyl]amino]benzoic acid C22 H22 Cl N3 O6 WWXZWJCMHLKBNT-BQYQJAHWSA-N
OGA	C [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.252 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.83	α = 90
b = 141.83	β = 90
c = 83.39	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Yang, C.-G., Gan, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22494693

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release