6E35 | pdb_00006e35

Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-Trp and cyanide, Northeast Structural Genomics Target HR6160

• PDB DOI: https://doi.org/10.2210/pdb6E35/pdb

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


• Deposited: 2018-07-13 Released: 2018-07-25 
• Deposition Author(s): Forouhar, F., Lewis-Ballester, A., Lew, S., Karkashon, S., Seetharaman, J., Lu, C., Hussain, M., Yeh, S.-R., Tong, L., Northeast Structural Genomics Consortium (NESG)
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-Trp and cyanide, Northeast Structural Genomics Target HR6160

Forouhar, F., Lewis-Ballester, A., Lew, S., Karkashon, S., Seetharaman, J., Lu, C., Hussain, M., Yeh, S.-R., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 97.44 kDa 
• Atom Count: 6,146 
• Modeled Residue Count: 731 
• Deposited Residue Count: 850 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indoleamine 2,3-dioxygenase 1	A, B	425	Homo sapiens	Mutation(s): 0  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 4 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
TRP	E [auth A], I [auth B]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
ZCW	F [auth A]	2-(1H-indol-3-yl)ethanol C10 H11 N O MBBOMCVGYCRMEA-UHFFFAOYSA-N
CYN	D [auth A], H [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.77	α = 90
b = 90.302	β = 90
c = 136.766	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
COMO	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Forouhar, F., Lewis-Ballester, A., Lew, S., Karkashon, S., Seetharaman, J., Lu, C., Hussain, M., Yeh, S.-R., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	P50 GM62413
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	U54 GM074958

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary