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- PDB-9esb: Holo IDO with a bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 9esb
TitleHolo IDO with a bound inhibitor
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Inhibitor / heme
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 / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsWicki, M. / Mac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SAR and cellular potency optimization of novel heme-binding IDO1 inhibitors
Authors: Cren, S. / Lotz, C. / Mac Sweeney, A. / Lange, R. / Kimmerlin, T.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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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)96,0556
Polymers94,1702
Non-polymers1,8844
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-53 kcal/mol
Surface area29860 Å2
Unit cell
Length a, b, c (Å)84.245, 92.135, 132.329
Angle α, β, γ (deg.)90, 90, 90
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: 47085.105 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 (E. coli) / 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-A1H6T / (~{R})-(6-chloranylimidazo[1,5-a]pyridin-5-yl)-(1-phenyl-1,2,3-triazol-4-yl)methanol


Mass: 325.752 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12ClN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.1 M MOPS/HEPES-Na 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 / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.1 Å / Num. obs: 94264 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rrim(I) all: 0.134 / Net I/σ(I): 9.3
Reflection shellResolution: 2.25→2.39 Å / Mean I/σ(I) obs: 0.84 / Num. unique obs: 15079 / CC1/2: 0.4 / Rrim(I) all: 1.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.249→46.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.262 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.255 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 2478 -RANDOM
Rwork0.239 ---
obs0.2405 49586 99.9 %-
Displacement parametersBiso mean: 50.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.2288 Å20 Å20 Å2
2--0.6309 Å20 Å2
3----0.402 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.249→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5849 0 132 68 6049
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076141HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.878361HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2053SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1110HARMONIC5
X-RAY DIFFRACTIONt_it6141HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion774SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4819SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion16.81
LS refinement shellResolution: 2.25→2.27 Å
RfactorNum. reflection% reflection
Rfree0.3743 50 -
Rwork0.3854 --
obs0.3849 992 94.32 %

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