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- PDB-7zv3: Crystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in comp... -

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Basic information

Entry
Database: PDB / ID: 7zv3
TitleCrystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferric heme and MMG-0472
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Dioxygenase / Heme-containing enzyme / Structure-based drug design / 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 / 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 / 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-(3-chloro-2-phenethylphenyl)-1H-1,2,3-triazole / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsRoehrig, U.F. / Reynaud, A. / Pojer, F. / Michielin, O. / Zoete, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Enzyme Inhib Med Chem / Year: 2022
Title: Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors.
Authors: Rohrig, U.F. / Majjigapu, S.R. / Vogel, P. / Reynaud, A. / Pojer, F. / Dilek, N. / Reichenbach, P. / Ascencao, K. / Irving, M. / Coukos, G. / Michielin, O. / Zoete, V.
History
DepositionMay 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 23, 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)97,0949
Polymers95,0092
Non-polymers2,0857
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-72 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.650, 97.419, 131.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 59 molecules

#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-RCT / 4-(3-chloro-2-phenethylphenyl)-1H-1,2,3-triazole / MMG-0472 / 5-[3-chloranyl-2-(2-phenylethyl)phenyl]-1H-1,2,3-triazole


Mass: 283.755 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14ClN3 / 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% PEG 4000, 0.2 M Lithium sulfate, 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: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.551→48.71 Å / Num. obs: 402628 / % possible obs: 99.5 % / Redundancy: 5.76 % / Rrim(I) all: 0.082 / Net I/σ(I): 15.2
Reflection shellResolution: 2.551→2.71 Å / Mean I/σ(I) obs: 1.89 / Num. unique obs: 11032 / Rrim(I) all: 0.768

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Processing

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

2d0t


Resolution: 2.551→48.709 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1820 4.92 %
Rwork0.1912 66467 -
obs0.1937 36916 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.84 Å2 / Biso mean: 60.7601 Å2 / Biso min: 35.51 Å2
Refinement stepCycle: final / Resolution: 2.551→48.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5915 0 142 52 6109
Biso mean--60.86 55.6 -
Num. residues----746
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5511-2.58610.36071050.3047238388
2.5861-2.6230.34781480.29542654100
2.623-2.66220.31211380.28982636100
2.6622-2.70380.39881560.2872687100
2.7038-2.74810.34981510.28842610100
2.7481-2.79550.35121290.27092719100
2.7955-2.84630.28911120.24742688100
2.8463-2.9010.39121550.2482676100
2.901-2.96030.27351440.23772643100
2.9603-3.02460.35121320.23932687100
3.0246-3.0950.2851370.23592707100
3.095-3.17230.33851310.25142656100
3.1723-3.25810.27581450.24712669100
3.2581-3.35390.35681410.24352683100
3.3539-3.46220.2821480.2412655100
3.4622-3.58590.28741540.21532633100
3.5859-3.72940.28711170.19712721100
3.7294-3.89910.23431290.1822672100
3.8991-4.10450.20631350.17722685100
4.1045-4.36150.19881430.1492640100
4.3615-4.69810.22751390.15132671100
4.6981-5.17040.16511420.14772671100
5.1704-5.91740.20341330.16232682100
5.9174-7.4510.19681210.16352696100
7.451-48.7090.15891580.13672643100

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