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- PDB-9uz4: Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) co... -

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Basic information

Entry
Database: PDB / ID: 9uz4
TitleCrystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with 5-methoxy-L-Trp
ComponentsMaltose/maltodextrin-binding periplasmic protein,Indoleamine 2,3-dioxygenase 2
KeywordsOXIDOREDUCTASE / HEM protein / Complex
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / indoleamine 2,3-dioxygenase activity / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / : / Tryptophan catabolism / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport ...Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / indoleamine 2,3-dioxygenase activity / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-tryptophan 2,3-dioxygenase activity / : / Tryptophan catabolism / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / immune system process / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / heme binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Indoleamine 2,3-dioxygenase / Indoleamine 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / : / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Maltose/maltodextrin-binding periplasmic protein / Indoleamine 2,3-dioxygenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTakahashi, A. / Inoue, T. / Fukuda, Y. / Adachi, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Febs J. / Year: 2026
Title: Human IDO2 exhibits unique binding affinities distinct to those of human IDO1.
Authors: Nogi, S. / Takahashi, A. / Murakami, S. / Adachi, N. / Fujimoto, T. / Fukuda, Y. / Yamashita, T. / Inoue, T. / Tsujino, H.
History
DepositionMay 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Indoleamine 2,3-dioxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,79017
Polymers86,8261
Non-polymers1,96416
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-23 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.253, 198.253, 94.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Indoleamine 2,3-dioxygenase 2 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IDO-2 / Indoleamine 2 / 3- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IDO-2 / Indoleamine 2 / 3-dioxygenase-like protein 1 / Indoleamine-pyrrole 2


Mass: 86825.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: malE, Z5632, ECs5017, IDO2, INDOL1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEY0, UniProt: Q6ZQW0, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 120 molecules

#3: Chemical ChemComp-A1A2Y / 5-methoxy-L-tryptophan


Mass: 234.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 6.15 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→49.56 Å / Num. obs: 73530 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 2.5→2.55 Å / Num. unique obs: 7145 / CC1/2: 0.525

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.38 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2801 3820 5.2 %
Rwork0.2464 --
obs0.2481 73497 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 133 105 6099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116132
X-RAY DIFFRACTIONf_angle_d1.1728315
X-RAY DIFFRACTIONf_dihedral_angle_d18.4432249
X-RAY DIFFRACTIONf_chiral_restr0.163911
X-RAY DIFFRACTIONf_plane_restr0.0091060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.43821580.42482549X-RAY DIFFRACTION100
2.53-2.560.43281200.41072535X-RAY DIFFRACTION100
2.57-2.60.43021350.38372588X-RAY DIFFRACTION100
2.6-2.640.4211530.37522554X-RAY DIFFRACTION100
2.64-2.680.37071570.3572565X-RAY DIFFRACTION100
2.68-2.720.3531340.34822558X-RAY DIFFRACTION100
2.72-2.760.33491500.33522538X-RAY DIFFRACTION100
2.76-2.810.36761520.31812527X-RAY DIFFRACTION100
2.81-2.860.33211350.30332588X-RAY DIFFRACTION100
2.86-2.920.31961310.30352563X-RAY DIFFRACTION100
2.92-2.980.32261410.29542568X-RAY DIFFRACTION100
2.98-3.040.31821340.28842588X-RAY DIFFRACTION100
3.04-3.110.32731550.29762523X-RAY DIFFRACTION100
3.11-3.190.34591560.30262564X-RAY DIFFRACTION100
3.19-3.280.29451360.2862594X-RAY DIFFRACTION100
3.28-3.370.28011670.26332547X-RAY DIFFRACTION100
3.37-3.480.29281540.25162557X-RAY DIFFRACTION100
3.48-3.610.30461160.2452622X-RAY DIFFRACTION100
3.61-3.750.26561390.22062569X-RAY DIFFRACTION100
3.75-3.920.26611380.22772611X-RAY DIFFRACTION100
3.92-4.130.23931230.21882583X-RAY DIFFRACTION100
4.13-4.380.23131350.20812587X-RAY DIFFRACTION100
4.39-4.720.26391310.20352628X-RAY DIFFRACTION100
4.72-5.20.25751670.21562575X-RAY DIFFRACTION100
5.2-5.950.24431280.24362633X-RAY DIFFRACTION100
5.95-7.490.27171360.24072639X-RAY DIFFRACTION100
7.49-45.380.27791390.24132724X-RAY DIFFRACTION100

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