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- PDB-8qv7: Crystal structure of human TDO with alpha-methyl-L-tryptophan -

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Basic information

Entry
Database: PDB / ID: 8qv7
TitleCrystal structure of human TDO with alpha-methyl-L-tryptophan
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 / 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 / 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: 2.928 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
DepositionOct 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024-
Revision 2.0Dec 4, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / pdbx_contact_author / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_validate_torsion / refine / refine_analyze / refine_hist / refine_ls_restr / refine_ls_shell / reflns / struct_conf
Item: _entity.pdbx_number_of_molecules / _pdbx_entry_details.has_protein_modification ..._entity.pdbx_number_of_molecules / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_overall_SU_R_free_Blow_DPI / _refine_analyze.Luzzati_coordinate_error_obs / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_obs / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_obs / _refine_ls_shell.percent_reflns_obs / _reflns.number_obs
Description: Model completeness
Details: The model has been refined at lower resolution following journal reviewer advice.
Provider: author / Type: Coordinate replacement

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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)170,91210
Polymers169,8544
Non-polymers1,0576
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18320 Å2
ΔGint-95 kcal/mol
Surface area52160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.285, 90.756, 132.774
Angle α, β, γ (deg.)90, 120.75, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Tryptophan 2,3-dioxygenase


Mass: 42463.594 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-ZIQ / alpha-methyl-L-tryptophan


Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20 mg/lml protein 50 mM HEPES pH 8.0 200 mM NaCl 2mM TCEP 10% glycerol

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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: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→114.1 Å / Num. obs: 40084 / % possible obs: 90.7 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.122 / Net I/σ(I): 3.2
Reflection shellResolution: 2.66→2.86 Å / Rmerge(I) obs: 0.559 / Num. unique obs: 1597 / CC1/2: 0.73 / Rpim(I) all: 0.354

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.928→41.35 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.866 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.401
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 1846 -RANDOM
Rwork0.2463 ---
obs0.2476 37715 94.1 %-
Displacement parametersBiso mean: 53.76 Å2
Baniso -1Baniso -2Baniso -3
1--7.1877 Å20 Å2-11.8825 Å2
2---2.6073 Å20 Å2
3---9.795 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.928→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9922 0 76 12 10010
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8313861HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3490SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1723HARMONIC5
X-RAY DIFFRACTIONt_it10236HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1303SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7712SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion18.58
LS refinement shellResolution: 2.93→2.95 Å
RfactorNum. reflection% reflection
Rfree0.4312 28 -
Rwork0.3329 --
obs0.3363 755 92.25 %

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