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- PDB-7zik: Crystal structure of human tryptophan hydroxylase 1 in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zik | ||||||
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Title | Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor LP533401 | ||||||
![]() | Tryptophan 5-hydroxylase 1 | ||||||
![]() | METAL BINDING PROTEIN / tryptophan hydroxylase / serotonin biosynthesis | ||||||
Function / homology | ![]() regulation of hemostasis / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / Serotonin and melatonin biosynthesis / aromatic amino acid metabolic process / serotonin biosynthetic process / platelet degranulation / bone remodeling / NGF-stimulated transcription / negative regulation of ossification ...regulation of hemostasis / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / Serotonin and melatonin biosynthesis / aromatic amino acid metabolic process / serotonin biosynthetic process / platelet degranulation / bone remodeling / NGF-stimulated transcription / negative regulation of ossification / response to immobilization stress / positive regulation of fat cell differentiation / mammary gland alveolus development / circadian rhythm / neuron projection / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schuetz, A. / Heinemann, U. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Design of Xanthine-Benzimidazole Derivatives as Novel and Potent Tryptophan Hydroxylase Inhibitors. Authors: Specker, E. / Matthes, S. / Wesolowski, R. / Schutz, A. / Grohmann, M. / Alenina, N. / Pleimes, D. / Mallow, K. / Neuenschwander, M. / Gogolin, A. / Weise, M. / Pfeifer, J. / Ziebart, N. / ...Authors: Specker, E. / Matthes, S. / Wesolowski, R. / Schutz, A. / Grohmann, M. / Alenina, N. / Pleimes, D. / Mallow, K. / Neuenschwander, M. / Gogolin, A. / Weise, M. / Pfeifer, J. / Ziebart, N. / Heinemann, U. / von Kries, J.P. / Nazare, M. / Bader, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.4 KB | Display | ![]() |
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PDB format | ![]() | 188.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 990.5 KB | Display | ![]() |
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Full document | ![]() | 1000.5 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zifC ![]() 7zigC ![]() 7zihC ![]() 7ziiC ![]() 7zijC ![]() 3hf8S S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Components
#1: Protein | Mass: 37424.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #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: 2.16 Å3/Da / Density % sol: 42.93 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 27% w/v PEG 3350, 0.1 M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.589→47.01 Å / Num. obs: 18984 / % possible obs: 97.48 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.5385969949 Å2 / Rmerge(I) obs: 0.1845 / Net I/σ(I): 6.77 |
Reflection shell | Resolution: 2.59→2.68 Å / Rmerge(I) obs: 0.7889 / Num. unique obs: 1763 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3hf8 Resolution: 2.58925907124→47.0095332779 Å / SU ML: 0.402330155809 / Cross valid method: FREE R-VALUE / σ(F): 1.9696969341 / Phase error: 28.2850266987
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9885529752 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58925907124→47.0095332779 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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