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- PDB-8r5r: Structure of apo TDO with a bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 8r5r
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 / tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding ...response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism / amino acid binding / oxygen binding / protein homotetramerization / heme binding / identical protein binding / metal ion 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: 3.078 Å
AuthorsWicki, M. / Mac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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

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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)173,75812
Polymers171,5124
Non-polymers2,2468
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17800 Å2
ΔGint-94 kcal/mol
Surface area50830 Å2
Unit cell
Length a, b, c (Å)91.738, 132.906, 137.495
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.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5.3 mg/ml (124 uM) protein containing 2 mM AMT and 1 mM inhibitor Reservoir solution: Morpheus II condition F8 5%(w/v) PEG 20K, 25%(w/v) 1,1,1-tris(hydroxymethyl)propane, 1%(w/v) NDSB 195,0. ...Details: 5.3 mg/ml (124 uM) protein containing 2 mM AMT and 1 mM inhibitor Reservoir solution: Morpheus II condition F8 5%(w/v) PEG 20K, 25%(w/v) 1,1,1-tris(hydroxymethyl)propane, 1%(w/v) NDSB 195,0.02M of each Monosaccharide II, 0.1M BES/TEA pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→76.31 Å / Num. obs: 27716 / % possible obs: 95.2 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.056 / Net I/σ(I): 9.8
Reflection shellResolution: 3.08→3.24 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1386 / CC1/2: 0.536 / Rsym value: 0.648 / % possible all: 60.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.078→50.83 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.474
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1368 -RANDOM
Rwork0.2267 ---
obs0.228 27708 87 %-
Displacement parametersBiso mean: 83.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.2922 Å20 Å20 Å2
2---2.2458 Å20 Å2
3----0.0465 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 3.078→50.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9839 0 156 7 10002
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710232HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8213877HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3408SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1732HARMONIC5
X-RAY DIFFRACTIONt_it10232HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1311SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8223SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion21.41
LS refinement shellResolution: 3.08→3.18 Å
RfactorNum. reflection% reflection
Rfree0.3248 37 -
Rwork0.3271 --
obs0.327 555 19.06 %

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