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Open data
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Basic information
Entry | Database: PDB / ID: 9ezj | ||||||
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Title | Apo human TDO in complex with a bound inhibitor (Cpd-4) | ||||||
![]() | Tryptophan 2,3-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / apo-TDO / heme / inhibitor | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wicki, M. / Mac Sweeney, A. | ||||||
Funding support | 1items
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![]() | ![]() 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. / Mueller, M. / Artico, N. / Ackerknecht, S. / Joesch, C. / Mac Sweeney, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 44 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47747.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZIQ / #3: Chemical | ChemComp-A1H8G / Mass: 532.631 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H36N4O5 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Morpheus 2, G11 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.612→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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 38.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.612→45.327 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.612→2.79 Å
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