7A62

Structure of human indoleamine-2,3-dioxygenase 1 (hIDO1) with a complete JK loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1.

Mirgaux, M.Leherte, L.Wouters, J.

(2020) Acta Crystallogr D Struct Biol 76: 1211-1221

  • DOI: 10.1107/S2059798320013510
  • Primary Citation of Related Structures:  
    7A62

  • PubMed Abstract: 
  • Indoleamine 2,3-dioxygenase 1 has sparked interest as an immunotherapeutic target in cancer research. Its structure includes a loop, named the JK-loop, that controls the orientation of the substrate or inhibitor within the active site. However, little has been reported about the crystal structure of this loop ...

    Indoleamine 2,3-dioxygenase 1 has sparked interest as an immunotherapeutic target in cancer research. Its structure includes a loop, named the JK-loop, that controls the orientation of the substrate or inhibitor within the active site. However, little has been reported about the crystal structure of this loop. In the present work, the conformation of the JK-loop is determined for the first time in the presence of the heme cofactor in the active site through X-ray diffraction experiments (2.44 Å resolution). Molecular-dynamics trajectories were also obtained to provide dynamic information about the loop according to the presence of cofactor. This new structural and dynamic information highlights the importance of the JK-loop in confining the labile heme cofactor to the active site.


    Organizational Affiliation

    Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Science (NARILIS), Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), University of Namur (UNamur), 61 Rue de Bruxelles, 5000 Namur, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Indoleamine 2,3-dioxygenase 1A, B, C, D405Homo sapiensMutation(s): 2 
Gene Names: IDO1IDOINDO
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14902
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
Q [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth B],
K [auth C],
L [auth C],
E [auth A],
G [auth B],
H [auth B],
K [auth C],
L [auth C],
N [auth D],
P [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
J [auth C],
O [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.96α = 90
b = 117.95β = 90
c = 216.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHASERphasing
MxCuBEdata collection
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedBelgium--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Advisory
  • Version 1.2: 2021-03-17
    Changes: Advisory