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Yorodumi- PDB-6pyy: Crystal Structure of human Tryptophan 2,3-dioxygenase in complex ... -
+Open data
-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 | |||||||||
Components | Tryptophan 2,3-dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Tryptophan Dioxygenase / PF-06840003 / Oxidoreductase / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex | |||||||||
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: 2.4 Å | |||||||||
Authors | Pham, K.N. / Lewis-Ballester, A. / Yeh, S.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pyy.cif.gz | 310.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pyy.ent.gz | 250.3 KB | Display | PDB format |
PDBx/mmJSON format | 6pyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/6pyy ftp://data.pdbj.org/pub/pdb/validation_reports/py/6pyy | HTTPS FTP |
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-Related structure data
Related structure data | 6pyzC 6pz1C 5ti9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: TDO2, TDO / Production host: Escherichia coli (E. coli) / References: UniProt: P48775, tryptophan 2,3-dioxygenase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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