+Open data
-Basic information
Entry | Database: PDB / ID: 8qv7 | ||||||
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Title | Crystal structure of human TDO with alpha-methyl-L-tryptophan | ||||||
Components | Tryptophan 2,3-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | ||||||
Authors | Wicki, M. / Mac Sweeney, A. | ||||||
Funding support | 1items
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Citation | 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qv7.cif.gz | 256.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qv7.ent.gz | 204.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/8qv7 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/8qv7 | HTTPS FTP |
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-Related structure data
Related structure data | 8r5qC 8r5rC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→114.1 Å / Num. obs: 31931 / % 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 shell | Resolution: 2.66→2.86 Å / Rmerge(I) obs: 0.559 / Num. unique obs: 1597 / CC1/2: 0.73 / Rpim(I) all: 0.354 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→34.46 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.848 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.438
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Displacement parameters | Biso mean: 34.36 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.66→34.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.86 Å
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