4U74

Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (G262A mutant)

PDB DOI: https://doi.org/10.2210/pdb4U74/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.220
R-Value Work: 0.171
R-Value Observed: 0.174

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 93.71 kDa
Atom Count: 6,421
Modelled Residue Count: 749
Deposited Residue Count: 812
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14902
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
NHE Query on NHE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
PIM Query on PIM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	4-PHENYL-1H-IMIDAZOLE C₉ H₈ N₂ XHLKOHSAWQPOFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
PIM	BindingDB: 4U74	IC50: min: 2.00e+4, max: 1.43e+5 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.220
R-Value Work: 0.171
R-Value Observed: 0.174
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.884	α = 90
b = 99.539	β = 90
c = 132.343	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PDB_EXTRACT	data extraction
REFMAC	refinement
HKL	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2015-09-02
Type: Initial release
Version 1.1: 2020-01-29
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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Help and Resources

4U74

Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (G262A mutant)

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)