7UI3 | pdb_00007ui3

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

• PDB DOI: https://doi.org/10.2210/pdb7UI3/pdb

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


• Deposited: 2022-03-28 Released: 2024-02-21 
• Deposition Author(s): Yeh, S.-R., Geeraerts, Z.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 
  0.278 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.245 (DCC) 

Starting Model: experimental

Literature

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

Yeh, S.-R., Geeraerts, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 181.6 kDa 
• Atom Count: 9,104 
• Modeled Residue Count: 1,207 
• Deposited Residue Count: 1,520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 2,3-dioxygenase	A, B, C, D	380	Homo sapiens	Mutation(s): 0  Gene Names: TDO2, TDO EC: 1.13.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens) Explore P48775  Go to UniProtKB:  P48775
PHAROS:  P48775 GTEx:  ENSG00000151790

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZIQ	E [auth A], F [auth B], G [auth C], H [auth D]	alpha-methyl-L-tryptophan C12 H14 N2 O2 ZTTWHZHBPDYSQB-LBPRGKRZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free:  0.278 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.245 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.855	α = 90
b = 156.264	β = 90
c = 88.986	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Coot	model building
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Yeh, S.-R., Geeraerts, Z.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115773
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM126297

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary