[English] 日本語
Yorodumi- PDB-3fun: Leukotriene A4 hydrolase in complex with {4-[(2R)-pyrrolidin-2-yl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fun | ||||||
---|---|---|---|---|---|---|---|
Title | Leukotriene A4 hydrolase in complex with {4-[(2R)-pyrrolidin-2-ylmethoxy]phenyl}(4-thiophen-3-ylphenyl)methanone | ||||||
Components | Leukotriene A-4 hydrolase | ||||||
Keywords | 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 | Function and homology information leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / 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 / protein metabolic process ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / 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 / protein metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / 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 / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Davies, D.R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fun.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fun.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fun_validation.pdf.gz | 721 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3fun_full_validation.pdf.gz | 726.7 KB | Display | |
Data in XML | 3fun_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 3fun_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fun ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fun | HTTPS FTP |
-Related structure data
Related structure data | 3ftsC 3ftuC 3ftvC 3ftwC 3ftxC 3ftyC 3fu0C 3fu3C 3fu5C 3fu6C 3fudC 3fueC 3fufC 3fuhC 3fuiC 3fujC 3fukC 3fumC 3fh7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|
-Non-polymers , 6 types, 450 molecules
#2: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#3: Chemical | ChemComp-YB / | ||
#4: Chemical | ChemComp-798 / { | ||
#5: Chemical | ChemComp-ACT / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % |
---|---|
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 10 mM {4-[(2R)-pyrrolidin-2-ylmethoxy]phenyl}(4-thiophen-3-ylphenyl)methanone, VAPOR DIFFUSION, ...Details: 13% PEG 8000, 100 mM Imidazole pH 6.5, 100 mM Na Acetate, 5 mM YbCl3, crystal soaked with 10 mM {4-[(2R)-pyrrolidin-2-ylmethoxy]phenyl}(4-thiophen-3-ylphenyl)methanone, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 93421 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.346 / % possible all: 98.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FH7 Resolution: 1.58→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.291 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 16.99 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.58→1.62 Å / Total num. of bins used: 20
|