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- PDB-3fuk: Leukotriene A4 hydrolase in complex with 1-[2-(1H-indol-5-yloxy)e... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fuk | ||||||
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Title | Leukotriene A4 hydrolase in complex with 1-[2-(1H-indol-5-yloxy)ethyl]piperidine-4-carboxylic acid | ||||||
![]() | Leukotriene A-4 hydrolase | ||||||
![]() | HYDROLASE / Leukotriene A4 Hydrolase / LTA4H / Fragment crystallography / Fragments of Life / FOL / Alternative splicing / Cytoplasm / Leukotriene biosynthesis / Metal-binding / Metalloprotease / Multifunctional enzyme / Polymorphism / Protease / Zinc | ||||||
Function / homology | ![]() leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / tripeptide aminopeptidase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / tripeptide aminopeptidase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) / protein metabolic process / epoxide hydrolase activity / leukotriene biosynthetic process / type I pneumocyte differentiation / response to zinc ion / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / lipid metabolic process / response to peptide hormone / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Davies, D.R. | ||||||
![]() | ![]() Title: Discovery of leukotriene A4 hydrolase inhibitors using metabolomics biased fragment crystallography. Authors: Davies, D.R. / Mamat, B. / Magnusson, O.T. / Christensen, J. / Haraldsson, M.H. / Mishra, R. / Pease, B. / Hansen, E. / Singh, J. / Zembower, D. / Kim, H. / Kiselyov, A.S. / Burgin, A.B. / ...Authors: Davies, D.R. / Mamat, B. / Magnusson, O.T. / Christensen, J. / Haraldsson, M.H. / Mishra, R. / Pease, B. / Hansen, E. / Singh, J. / Zembower, D. / Kim, H. / Kiselyov, A.S. / Burgin, A.B. / Gurney, M.E. / Stewart, L.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.5 KB | Display | ![]() |
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PDB format | ![]() | 109.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ftsC ![]() 3ftuC ![]() 3ftvC ![]() 3ftwC ![]() 3ftxC ![]() 3ftyC ![]() 3fu0C ![]() 3fu3C ![]() 3fu5C ![]() 3fu6C ![]() 3fudC ![]() 3fueC ![]() 3fufC ![]() 3fuhC ![]() 3fuiC ![]() 3fujC ![]() 3fumC ![]() 3funC ![]() 3fh7S 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69363.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 356 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/58Z.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/58Z.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-YB / | ||
#4: Chemical | ChemComp-58Z / | ||
#5: Chemical | ChemComp-ACT / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 13% PEG 8000, 100 mM Imidazole pH 6.5, 100 mM Na Acetate, 5 mM YbCl3, crystal soaked in 13% PEG 8000, 100 mM Imidazole, 100 mM Sodium acetate, 150 mM NaCl, 25 mM 1-[2-(1H-indol-5-yloxy)ethyl] ...Details: 13% PEG 8000, 100 mM Imidazole pH 6.5, 100 mM Na Acetate, 5 mM YbCl3, crystal soaked in 13% PEG 8000, 100 mM Imidazole, 100 mM Sodium acetate, 150 mM NaCl, 25 mM 1-[2-(1H-indol-5-yloxy)ethyl]piperidine-4-carboxylic acid, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 49997 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.743 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3FH7 Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.639 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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