6E42

CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) in complex with ferric heme and 4-Chlorophenyl imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.103 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form.

Luo, S.Xu, K.Xiang, S.Chen, J.Chen, C.Guo, C.Tong, Y.Tong, L.

(2018) Acta Crystallogr F Struct Biol Commun 74: 717-724

  • DOI: 10.1107/S2053230X18012955
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various i ...

    Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2-2.3 Å. Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported. One of these crystal forms diffracted to 1.5 Å resolution and can be readily used for soaking experiments to determine high-resolution structures of IDO1 in complex with the substrate tryptophan or inhibitors that coordinate the heme. In addition, this mutant was used to produce crystals of a complex with an inhibitor that targets the apo form of the enzyme under the same conditions; the structure of this complex was determined at 1.7 Å resolution. Overall, this mutant represents a robust platform for determining the structures of inhibitor and substrate complexes of IDO1 at high resolution.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Indoleamine 2,3-dioxygenase 1
A, B, C, D
405Homo sapiensMutation(s): 2 
Gene Names: IDO1 (IDO, INDO)
EC: 1.13.11.52
Find proteins for P14902 (Homo sapiens)
Go to Gene View: IDO1
Go to UniProtKB:  P14902
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HQJ
Query on HQJ

Download SDF File 
Download CCD File 
A, B, C, D
4-(3-chlorophenyl)-1H-imidazole
C9 H7 Cl N2
YAJYVAFOVNSPBQ-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.103 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.742α = 90.00
b = 197.878β = 90.00
c = 113.019γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-07-16 
  • Released Date: 2018-11-14 
  • Deposition Author(s): Luo, S., Tong, L.

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release