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- PDB-9esd: Holo TDO with a bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 9esd
TitleHolo TDO with a bound inhibitor
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Inhibitor / heme
Function / homology
Function and homology information


ommochrome biosynthetic process / compound eye pigmentation / Tryptophan catabolism / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / kynurenine metabolic process / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / L-tryptophan catabolic process / protein homotetramerization ...ommochrome biosynthetic process / compound eye pigmentation / Tryptophan catabolism / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / kynurenine metabolic process / tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / L-tryptophan catabolic process / protein homotetramerization / heme binding / metal ion binding
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
Chem-5PK / PROTOPORPHYRIN IX CONTAINING FE / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 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: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
C: Tryptophan 2,3-dioxygenase
D: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,81412
Polymers173,2194
Non-polymers3,5958
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27250 Å2
ΔGint-199 kcal/mol
Surface area53670 Å2
Unit cell
Length a, b, c (Å)143.736, 143.736, 141.218
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Tryptophan 2,3-dioxygenase / TDO / Protein vermilion / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TO / TRPO / ...TDO / Protein vermilion / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TO / TRPO / Tryptophan pyrrolase / Tryptophanase


Mass: 43304.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: v, CG5163 / Production host: Escherichia coli (E. coli) / References: UniProt: P20351, tryptophan 2,3-dioxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-5PK / (1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol


Mass: 282.380 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H22N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0M Na Malonate pH 5.00, 0.1M Na Acetate pH4.50, 2% PEG 20,000

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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: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.103→47.1 Å / Num. obs: 189538 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rrim(I) all: 0.149 / Net I/σ(I): 8.24
Reflection shellResolution: 2.103→2.23 Å / Mean I/σ(I) obs: 0.69 / Num. unique obs: 30427 / CC1/2: 0.225 / Rrim(I) all: 2.23

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.103→47.05 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4796 -RANDOM
Rwork0.2325 ---
obs0.2336 95909 100 %-
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.1539 Å20 Å20 Å2
2---0.1539 Å20 Å2
3---0.3079 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.103→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11030 0 256 58 11344
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811577HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8115642HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4247SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2075HARMONIC5
X-RAY DIFFRACTIONt_it11577HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1434SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8632SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion15.64
LS refinement shellResolution: 2.103→2.12 Å
RfactorNum. reflection% reflection
Rfree0.3586 96 -
Rwork0.3653 --
obs--98.89 %

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