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- PDB-7ah4: Crystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in comp... -

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Basic information

Entry
Database: PDB / ID: 7ah4
TitleCrystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferric heme and MMG-0363
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 / positive regulation of chronic inflammatory response / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process ... indoleamine 2,3-dioxygenase / positive regulation of chronic inflammatory response / indoleamine 2,3-dioxygenase activity / kynurenic acid biosynthetic process / smooth muscle contractile fiber / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / stereocilium bundle / positive regulation of type 2 immune response / L-tryptophan catabolic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / T cell proliferation / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytoplasm / cytosol
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-chloranyl-2-(2~{H}-1,2,3-triazol-4-yl)aniline / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)97,0208
Polymers95,0092
Non-polymers2,0116
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-45 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.571, 97.422, 131.739
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) / 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-RCN / 4-chloranyl-2-(2~{H}-1,2,3-triazol-4-yl)aniline / MMG-0363


Mass: 194.621 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7ClN4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% PEG 4000, 0.1 M Tris pH 7.5, 0.2 M Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / 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: 2.401→48.711 Å / Num. obs: 44167 / % possible obs: 99.87 % / Redundancy: 7.4 % / Rrim(I) all: 0.058 / Net I/σ(I): 23.67
Reflection shellResolution: 2.401→2.49 Å / Num. unique obs: 30540 / Rrim(I) all: 0.7056

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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: 2.401→48.711 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1999 4.53 %
Rwork0.2141 42161 -
obs0.2157 44160 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.19 Å2 / Biso mean: 57.8691 Å2 / Biso min: 31.93 Å2
Refinement stepCycle: final / Resolution: 2.401→48.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 164 112 6173
Biso mean--47.28 54.24 -
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 (%)
2.401-2.46080.31691380.3009292398
2.4608-2.52730.32771390.29322936100
2.5273-2.60170.33841430.28083011100
2.6017-2.68560.30551410.29022968100
2.6856-2.78160.33051410.26742977100
2.7816-2.8930.27441420.26992995100
2.893-3.02460.27881410.27632980100
3.0246-3.1840.35741420.27392998100
3.184-3.38350.31431430.26343003100
3.3835-3.64460.31261420.23633014100
3.6446-4.01130.23821430.20213011100
4.0113-4.59130.19531460.17543051100
4.5913-5.78310.21621450.17863090100
5.7831-48.7110.17591530.163204100

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