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- PDB-6pyy: Crystal Structure of human Tryptophan 2,3-dioxygenase in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pyy | |||||||||
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Title | Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PF-06840003 in Active Site and Exo site | |||||||||
![]() | Tryptophan 2,3-dioxygenase | |||||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Tryptophan Dioxygenase / PF-06840003 / Oxidoreductase / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Pham, K.N. / Lewis-Ballester, A. / Yeh, S.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. Authors: Pham, K.N. / Lewis-Ballester, A. / Yeh, S.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.8 KB | Display | ![]() |
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PDB format | ![]() | 250.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pyzC ![]() 6pz1C ![]() 5ti9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 45182.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-H7S / ( #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: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 298 K / Method: microbatch Details: 50 mM Sodium Citrate (pH 5.6), 2% Tacsimate (pH 5.0) 5% PEG 3350 PH range: 5.0-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Mar 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.9 Å / Num. obs: 77243 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 53.3 Å2 / CC1/2: 1 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.4→2.53 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11127 / CC1/2: 0.39 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TI9 Resolution: 2.4→29.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.849 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.236 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.43 Å2 / Biso mean: 53.319 Å2 / Biso min: 24.02 Å2
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Refinement step | Cycle: final / Resolution: 2.4→29.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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