4U72 | pdb_00004u72

Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)

• PDB DOI: https://doi.org/10.2210/pdb4U72/pdb

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


• Deposited: 2014-07-30 Released: 2015-09-02 
• Deposition Author(s): Sugimoto, H., Horitani, M., Kometani, E., Shiro, Y.
• Funding Organization(s): JSPS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Conformation and Mobility of Active Site Loop is Critical for Substrate Binding and Inhibition in Human Indoleamine 2,3-Dioxygenase

Horitani, M., Kometani, E., Vottero, E., Otsuki, T., Shiro, Y., Sugimoto, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 93.66 kDa 
• Atom Count: 6,471 
• Modeled Residue Count: 749 
• Deposited Residue Count: 812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indoleamine 2,3-dioxygenase 1	A, B	406	Homo sapiens	Mutation(s): 1  Gene Names: IDO1, IDO, INDO EC: 1.13.11.52
UniProt & NIH Common Fund Data Resources
Find proteins for P14902 (Homo sapiens) Explore P14902  Go to UniProtKB:  P14902
PHAROS:  P14902 GTEx:  ENSG00000131203

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NHE	E [auth A], F [auth A], I [auth B], J [auth B]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
PIM	D [auth A], H [auth B]	4-PHENYL-1H-IMIDAZOLE C9 H8 N2 XHLKOHSAWQPOFO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PIM	BindingDB:  4U72	IC50: min: 2.00e+4, max: 1.43e+5 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.971	α = 90
b = 98.89	β = 90
c = 131.582	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
HKL	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Sugimoto, H., Horitani, M., Kometani, E., Shiro, Y.

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Funding Organization	Location	Grant Number
JSPS	Japan	22105012
JSPS	Japan	24687015
JSPS	Japan	19770094
JSPS	Japan	20050033

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary