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- PDB-3ful: Leukotriene A4 hydrolase in complex with pyridin-4-yl[4-(2-pyrrol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ful | ||||||
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Title | Leukotriene A4 hydrolase in complex with pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone | ||||||
![]() | Leukotriene A-4 hydrolase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Leukotriene A4 Hydrolase / LTA4H / Fragment crystallography / Fragments of Life / FOL / Hydrolase-hydrolase inhibitor complex / Leukotriene biosynthesis / Metal-binding / Metalloprotease / Multifunctional enzyme / Protease | ||||||
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 4-[(2S)-2-{[4-(4-chlorophenoxy)phenoxy]methyl}-1-pyrrolidinyl]butanoic acid (DG-051) as a novel leukotriene A4 hydrolase inhibitor of leukotriene B4 biosynthesis. Authors: Sandanayaka, V. / Mamat, B. / Mishra, R.K. / Winger, J. / Krohn, M. / Zhou, L.M. / Keyvan, M. / Enache, L. / Sullins, D. / Onua, E. / Zhang, J. / Halldorsdottir, G. / Sigthorsdottir, H. / ...Authors: Sandanayaka, V. / Mamat, B. / Mishra, R.K. / Winger, J. / Krohn, M. / Zhou, L.M. / Keyvan, M. / Enache, L. / Sullins, D. / Onua, E. / Zhang, J. / Halldorsdottir, G. / Sigthorsdottir, H. / Thorlaksdottir, A. / Sigthorsson, G. / Thorsteinnsdottir, M. / Davies, D.R. / Stewart, L.J. / Zembower, D.E. / Andresson, T. / Kiselyov, A.S. / Singh, J. / Gurney, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.4 KB | Display | ![]() |
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PDB format | ![]() | 105.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fh5C ![]() 3fh7SC ![]() 3fh8C ![]() 3fheC ![]() 3ftzC 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 , 5 types, 155 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/52D.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/52D.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-52D / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % |
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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 with 25 mM pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. obs: 27142 / % possible obs: 98.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.39→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.707 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3FH7 Resolution: 2.39→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.663 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.262 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.45 Å / Total num. of bins used: 20
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