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Yorodumi- PDB-3ftz: Leukotriene A4 hydrolase in complex with fragment 2-(pyridin-3-yl... -
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-Basic information
Entry | Database: PDB / ID: 3ftz | ||||||
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Title | Leukotriene A4 hydrolase in complex with fragment 2-(pyridin-3-ylmethoxy)aniline | ||||||
Components | Leukotriene A-4 hydrolase | ||||||
Keywords | 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 | Function and homology information 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 / peptide catabolic process / response to zinc ion / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Davies, D.R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ftz.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ftz.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ftz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ftz_validation.pdf.gz | 460.1 KB | Display | wwPDB validaton report |
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Full document | 3ftz_full_validation.pdf.gz | 464.1 KB | Display | |
Data in XML | 3ftz_validation.xml.gz | 26 KB | Display | |
Data in CIF | 3ftz_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ftz ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ftz | HTTPS FTP |
-Related structure data
Related structure data | 3fh5C 3fh7SC 3fh8C 3fheC 3fulC 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
-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.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI/pRARE / References: UniProt: P09960, leukotriene-A4 hydrolase |
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-Non-polymers , 6 types, 368 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-YB / | ||||
#4: Chemical | ChemComp-848 / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.59 % |
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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, 5 mM 2-(pyridin-3-ylmethoxy) ...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, 5 mM 2-(pyridin-3-ylmethoxy)aniline, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99994 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99994 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 43773 / % possible obs: 93.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.54 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FH7 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.504 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.165 / 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: 21.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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