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Open data
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Basic information
Entry | Database: PDB / ID: 8r5q | ||||||
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Title | Structure of apo TDO with a bound inhibitor | ||||||
![]() | Tryptophan 2,3-dioxygenase![]() | ||||||
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Function / homology | ![]() response to nitroglycerin / tryptophan catabolic process to acetyl-CoA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wicki, M. / Mac Sweeney, A. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.6 KB | Display | ![]() |
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PDB format | ![]() | 204.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8qv7C ![]() 8r5rC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 42878.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-Y5N / #3: Chemical | ChemComp-ZIQ / #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: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 5.3 mg/ml (124 uM) protein containing 2 mM AMT and 1 mM inhibitor, 12.5 % PEG 4000, 20% hexanetriol, 20 mM each of arginine, threonine, histidine, 5-hydroxylysine, trans-4-hydroxy-L-proline, 100 mM AMPD pH 8.5 |
-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: Sep 24, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.62→94.8 Å / Num. obs: 39729 / % possible obs: 94.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.101 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.62→2.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 16059 / CC1/2: 0.61 / % possible all: 58.3 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Displacement parameters | Biso mean: 78.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→75.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.77 Å
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