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- PDB-9ezj: Apo human TDO in complex with a bound inhibitor (Cpd-4) -

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Basic information

Entry
Database: PDB / ID: 9ezj
TitleApo human TDO in complex with a bound inhibitor (Cpd-4)
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / apo-TDO / heme / inhibitor
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 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 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
: / alpha-methyl-L-tryptophan / Tryptophan 2,3-dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.612 Å
AuthorsWicki, M. / Mac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionApr 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)193,99212
Polymers190,9894
Non-polymers3,0048
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.793, 156.159, 90.655
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 47747.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDO2, TDO / Production host: Escherichia coli (E. coli) / References: UniProt: P48775, tryptophan 2,3-dioxygenase
#2: 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
#3: Chemical
ChemComp-A1H8G / ethyl (9~{R})-2-methoxy-4-oxidanylidene-9-[[(1~{S})-1-phenylethyl]-[(2-propan-2-ylphenyl)carbamoyl]amino]-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidine-3-carboxylate


Mass: 532.631 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H36N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Morpheus 2, G11

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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: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.612→45.327 Å / Num. obs: 43550 / % possible obs: 94.2 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.269 / Rrim(I) all: 0.307 / Net I/σ(I): 6
Reflection shellResolution: 2.612→2.868 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.382 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2177 / CC1/2: 0.685 / Rrim(I) all: 1.502

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.612→45.327 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.884 / SU R Cruickshank DPI: 1.765 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.409 / SU Rfree Blow DPI: 0.446 / SU Rfree Cruickshank DPI: 0.461
RfactorNum. reflection% reflectionSelection details
Rfree0.3302 2171 -RANDOM
Rwork0.2979 ---
obs0.2995 43550 74.7 %-
Displacement parametersBiso mean: 38.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.9188 Å20 Å20 Å2
2---0.7587 Å20 Å2
3----0.1601 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.612→45.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10031 0 220 8 10259
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710520HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8114265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3602SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1863HARMONIC5
X-RAY DIFFRACTIONt_it10520HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1327SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8074SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion18.2
LS refinement shellResolution: 2.612→2.79 Å
RfactorNum. reflection% reflection
Rfree0.4818 34 -
Rwork0.3735 --
obs--8.58 %

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