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- PDB-9foh: Crystal structure of human IDO1 in complex with iDeg-2 -

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Basic information

Entry
Database: PDB / ID: 9foh
TitleCrystal structure of human IDO1 in complex with iDeg-2
ComponentsIndoleamine 2,3-dioxygenase 1
KeywordsOXIDOREDUCTASE / Indoleamine 2 / 3-dioxygenase 1 / heme-binding protein
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
: / TRIETHYLENE GLYCOL / Indoleamine 2,3-dioxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLucas, B. / Lucas, M. / Ziegler, S. / Waldmann, H. / Gasper, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To be published
Title: Crystal structure of human IDO1 in complex with iDeg-2
Authors: Lucas, B.
History
DepositionJun 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,04910
Polymers45,3671
Non-polymers1,6829
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint21 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.840, 110.420, 36.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 45367.156 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 252 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-A1IEE / ((3aS,4R,6R,7aS)-2-((4-(tert-butyl)phenyl)sulfonyl)-5,5-dimethyloctahydro-3aH-4,6-methanoisoindol-3a-yl)methyl (4-iodophenyl)carbamate / [(1~{R},2~{S},6~{S},8~{R})-4-(4-~{tert}-butylphenyl)sulfonyl-9,9-dimethyl-4-azatricyclo[6.1.1.0^{2,6}]decan-2-yl]methyl ~{N}-(4-iodophenyl)carbamate


Mass: 636.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37IN2O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.95 / Details: 0.05 M MES, 39% v/v PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→38.01 Å / Num. obs: 56433 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.139 / Net I/σ(I): 11.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.642.38441670.4612.51
1.64-1.691.99439590.5742.081
1.69-1.741.69139330.6931.7581
1.74-1.791.32637720.7991.381
1.79-1.851.05536560.841.0991
1.85-1.910.79136030.9290.8231
1.91-1.980.59234260.9540.6161
1.98-2.070.4432910.9770.4571
2.07-2.160.34131980.9820.3551
2.16-2.260.25830780.9890.2681
2.26-2.390.20728990.9930.2151
2.39-2.530.17227590.9940.1791
2.53-2.70.13426040.9960.1391
2.7-2.920.10624300.9970.1111
2.92-3.20.08722480.9980.091
3.2-3.580.06720640.9980.071
3.58-4.130.05818180.9980.0611
4.13-5.060.05215650.9990.0541
5.06-7.160.05512340.9980.0571
7.16-38.010.0547290.9980.0571

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.01 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 2822 5 %
Rwork0.1712 --
obs0.1721 56423 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 102 243 3172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053115
X-RAY DIFFRACTIONf_angle_d0.7594234
X-RAY DIFFRACTIONf_dihedral_angle_d10.856466
X-RAY DIFFRACTIONf_chiral_restr0.042459
X-RAY DIFFRACTIONf_plane_restr0.012536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.38121400.35692652X-RAY DIFFRACTION100
1.63-1.660.35131390.32532639X-RAY DIFFRACTION100
1.66-1.690.28551360.28852603X-RAY DIFFRACTION100
1.69-1.720.23741420.26722683X-RAY DIFFRACTION100
1.72-1.760.26751380.2352622X-RAY DIFFRACTION100
1.76-1.80.26311400.22392660X-RAY DIFFRACTION100
1.8-1.850.26221380.21352621X-RAY DIFFRACTION100
1.85-1.90.24631400.20062658X-RAY DIFFRACTION100
1.9-1.950.20381390.19392640X-RAY DIFFRACTION100
1.95-2.020.22311410.19542675X-RAY DIFFRACTION100
2.02-2.090.20011400.18232660X-RAY DIFFRACTION100
2.09-2.170.17581400.16222659X-RAY DIFFRACTION100
2.17-2.270.2111410.15672688X-RAY DIFFRACTION100
2.27-2.390.16291400.14822654X-RAY DIFFRACTION100
2.39-2.540.18271410.15222684X-RAY DIFFRACTION100
2.54-2.740.18651420.15872692X-RAY DIFFRACTION100
2.74-3.010.16971430.15822734X-RAY DIFFRACTION100
3.01-3.450.17541430.16422703X-RAY DIFFRACTION100
3.45-4.340.15481450.13892766X-RAY DIFFRACTION100
4.34-38.010.17181540.1652908X-RAY DIFFRACTION100

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