+Open data
-Basic information
Entry | Database: PDB / ID: 8vzv | |||||||||
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Title | Human TDO (hTDO) in complex with LM10 | |||||||||
Components | Tryptophan 2,3-dioxygenase | |||||||||
Keywords | CYTOSOLIC PROTEIN / Human TDO / hTDO / LM10 | |||||||||
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: 2.29 Å | |||||||||
Authors | Ishigami, I. / Yeh, S.-R. / Lewis-Ballester, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Structural Insights into Protein-Inhibitor Interactions in Human Tryptophan Dioxygenase. Authors: Geeraerts, Z. / Ishigami, I. / Lewis-Ballester, A. / Pham, K.N. / Kozlova, A. / Mathieu, C. / Frederick, R. / 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 | 8vzv.cif.gz | 317.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vzv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vzv_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 8vzv_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 8vzv_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 8vzv_validation.cif.gz | 71.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/8vzv ftp://data.pdbj.org/pub/pdb/validation_reports/vz/8vzv | HTTPS FTP |
-Related structure data
Related structure data | 7lu7C 8vtqC 8vugC 8w1hC 8w2kC 9at2C 9b17C 9b1qC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: GLY / Beg label comp-ID: GLY
NCS ensembles :
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-Components
#1: Protein | Mass: 45182.535 Da / Num. of mol.: 4 / Fragment: UNP residues 18-389 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-ZIQ / #4: Chemical | Mass: 229.213 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H8FN5 / Feature type: SUBJECT OF INVESTIGATION #5: 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: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 50 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350 |
-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 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→52.31 Å / Num. obs: 85859 / % possible obs: 97.258 % / Redundancy: 6.6 % / Rpim(I) all: 0.076 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.29→2.41 Å / Rmerge(I) obs: 1.512 / Num. unique obs: 84922 / CC1/2: 0.139 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→30.002 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.192 / SU B: 10.066 / SU ML: 0.214 / Average fsc free: 0.8276 / Average fsc work: 0.8375 / Cross valid method: FREE R-VALUE / ESU R: 0.287 / ESU R Free: 0.216 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.005 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→30.002 Å
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Refine LS restraints |
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