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- PDB-8r5q: Structure of apo TDO with a bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 8r5q
TitleStructure of apo TDO with a bound inhibitor
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / inhibitor / apo / heme
Function / homology
Function and homology information


response to nitroglycerin / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / L-tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to L-kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding ...response to nitroglycerin / L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / L-tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to L-kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Tryptophan 2,3-dioxygenase / Tryptophan 2,3-dioxygenase / Tryptophan/Indoleamine 2,3-dioxygenase-like
Similarity search - Domain/homology
Chem-Y5N / alpha-methyl-L-tryptophan / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsWicki, M. / Mac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Sci Rep / Year: 2024
Title: Discovery and binding mode of small molecule inhibitors of the apo form of human TDO2.
Authors: Lotz-Jenne, C. / Lange, R. / Cren, S. / Bourquin, G. / Goglia, L. / Kimmerlin, T. / Wicki, M. / Muller, M. / Artico, N. / Ackerknecht, S. / Pfaff, P. / Joesch, C. / Mac Sweeney, A.
#1: Journal: Biorxiv / Year: 2024
Title: Discovery and binding mode of a small molecule inhibitor of the apo form of human TDO2
Authors: Lotz-Jenne, C. / Lange, R. / Cren, S. / Bourquin, G. / Goglia, L. / Kimmerlin, T. / Wicki, M. / Mueller, M. / Artico, N. / Ackerknecht, S. / Joesch, C. / Mac Sweeney, A.
History
DepositionNov 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)173,75812
Polymers171,5124
Non-polymers2,2468
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17550 Å2
ΔGint-94 kcal/mol
Surface area51770 Å2
Unit cell
Length a, b, c (Å)91.33, 132.49, 135.57
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan 2,3-dioxygenase


Mass: 42878.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDO2 / Production host: Escherichia coli (E. coli) / Strain (production host): RP523 / References: UniProt: P48775
#2: Chemical
ChemComp-Y5N / 3-chloranyl-~{N}-[(1~{S})-1-(6-chloranylpyridin-3-yl)-2-phenyl-ethyl]aniline


Mass: 343.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H16Cl2N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZIQ / alpha-methyl-L-tryptophan


Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5.3 mg/ml (124 uM) protein containing 2 mM AMT and 1 mM inhibitor, 12.5 % PEG 4000, 20% hexanetriol, 20 mM each of arginine, threonine, histidine, 5-hydroxylysine, trans-4-hydroxy-L-proline, 100 mM AMPD pH 8.5

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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: Sep 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→94.8 Å / Num. obs: 39729 / % possible obs: 94.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.101 / Net I/σ(I): 14.5
Reflection shellResolution: 2.62→2.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 16059 / CC1/2: 0.61 / % possible all: 58.3

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→75.75 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / SU R Blow DPI: 2.302 / SU Rfree Blow DPI: 0.367
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 1876 -RANDOM
Rwork0.2544 ---
obs0.255 39723 79.2 %-
Displacement parametersBiso mean: 78.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.344 Å20 Å20 Å2
2--0.3783 Å20 Å2
3---0.9657 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.62→75.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9799 0 156 5 9960
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710191HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8513825HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3379SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1726HARMONIC5
X-RAY DIFFRACTIONt_it10191HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1311SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7670SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion20.52
LS refinement shellResolution: 2.62→2.77 Å
RfactorNum. reflection% reflection
Rfree0.4097 35 -
Rwork0.3425 --
obs0.3452 795 10.62 %

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