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- PDB-7ah6: Crystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in comp... -

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Basic information

Entry
Database: PDB / ID: 7ah6
TitleCrystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferric heme and MMG-0752
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Dioxygenase / Heme-containing enzyme / Structure-based drug design / IDO1 inhibitor / Triazole / Small-molecule inhibitor
Function / homology
Function and homology information


indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / stereocilium bundle / tryptophan catabolic process to kynurenine / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / stereocilium bundle / tryptophan catabolic process to kynurenine / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / positive regulation of T cell apoptotic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / negative regulation of T cell proliferation / T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase signature 1. / Indoleamine 2,3-dioxygenase signature 2. / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 4-bromanyl-2-(4~{H}-1,2,4-triazol-3-yl)aniline / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å
AuthorsRoehrig, U.F. / Reynaud, A. / Pojer, F. / Michielin, O. / Zoete, V.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors.
Authors: Rohrig, U.F. / Majjigapu, S.R. / Reynaud, A. / Pojer, F. / Dilek, N. / Reichenbach, P. / Ascencao, K. / Irving, M. / Coukos, G. / Vogel, P. / Michielin, O. / Zoete, V.
History
DepositionSep 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Indoleamine 2,3-dioxygenase 1
B: Indoleamine 2,3-dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2909
Polymers95,0092
Non-polymers2,2817
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-44 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.811, 91.723, 127.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Indoleamine 2,3-dioxygenase 1 / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase


Mass: 47504.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta DE3 / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-RCW / 4-bromanyl-2-(4~{H}-1,2,4-triazol-3-yl)aniline / MMG-0752


Mass: 239.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7BrN4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 4.0 M Sodium formate, 0.1 M Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.998→45.862 Å / Num. obs: 20720 / % possible obs: 99.68 % / Redundancy: 8.7 % / Rrim(I) all: 0.1081 / Net I/σ(I): 18.09
Reflection shellResolution: 2.998→3.11 Å / Num. unique obs: 18198 / Rrim(I) all: 0.8216

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d0t

2d0t


Resolution: 2.998→45.862 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 1996 9.64 %
Rwork0.222 18719 -
obs0.2273 20715 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.65 Å2 / Biso mean: 70.7138 Å2 / Biso min: 32.72 Å2
Refinement stepCycle: final / Resolution: 2.998→45.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5899 0 144 0 6043
Biso mean--56.71 --
Num. residues----743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.998-3.07280.42311250.2931130697
3.0728-3.15590.37591490.26971303100
3.1559-3.24880.34551330.2831316100
3.2488-3.35360.34081500.26631311100
3.3536-3.47340.32941350.281315100
3.4734-3.61240.37971520.25491314100
3.6124-3.77680.32011400.25041320100
3.7768-3.97580.32391360.2298134399
3.9758-4.22470.29681410.20341327100
4.2247-4.55060.24651370.20261342100
4.5506-5.00810.24461550.18991331100
5.0081-5.73160.24571470.21261363100
5.7316-7.21660.23021420.21781379100
7.2166-45.8620.21061540.18921449100

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