+Open data
-Basic information
Entry | Database: PDB / ID: 2r59 | ||||||
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Title | Leukotriene A4 hydrolase complexed with inhibitor RB3041 | ||||||
Components | Leukotriene A-4 hydrolase | ||||||
Keywords | HYDROLASE / transition state / analogue peptide / hydrolysis / Alternative splicing / Cytoplasm / Leukotriene biosynthesis / Metal-binding / Metalloprotease / Multifunctional enzyme / Protease / Zinc | ||||||
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 / Resolution: 1.89 Å | ||||||
Authors | Tholander, F. / Haeggstrom, J.Z. / Thunnissen, M. / Muroya, A. / Roques, B.P. / Fournie-Zaluski, M.C. | ||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: Structure-based dissection of the active site chemistry of leukotriene a4 hydrolase: implications for m1 aminopeptidases and inhibitor design. Authors: Tholander, F. / Muroya, A. / Roques, B.P. / Fournie-Zaluski, M.C. / Thunnissen, M.M. / Haeggstrom, J.Z. #1: Journal: Proteins / Year: 2007 Title: Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase. Authors: Tholander, F. / Haeggstrom, J.Z. #2: Journal: J.Biol.Chem. / Year: 2004 Title: Leukotriene A4 hydrolase: identification of a common carboxylate recognition site for the epoxide hydrolase and aminopeptidase substrates. Authors: Rudberg, P.C. / Tholander, F. / Andberg, M. / Thunnissen, M.M. / Haeggstrom, J.Z. #3: Journal: J.Biol.Chem. / Year: 2002 Title: Leukotriene A4 hydrolase/aminopeptidase. Glutamate 271 is a catalytic residue with specific roles in two distinct enzyme mechanisms. Authors: Rudberg, P.C. / Tholander, F. / Thunnissen, M.M. / Haeggstrom, J.Z. #4: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2002 Title: Leukotriene A4 hydrolase: selective abrogation of leukotriene B4 formation by mutation of aspartic acid 375. Authors: Rudberg, P.C. / Tholander, F. / Thunnissen, M.M. / Samuelsson, B. / Haeggstrom, J.Z. #5: Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation. Authors: Thunnissen, M.M. / Nordlund, P. / Haeggstrom, J.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r59.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r59.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r59_validation.pdf.gz | 800.8 KB | Display | wwPDB validaton report |
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Full document | 2r59_full_validation.pdf.gz | 807.8 KB | Display | |
Data in XML | 2r59_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 2r59_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/2r59 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r59 | HTTPS FTP |
-Related 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: 70061.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: pT7T3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P09960, leukotriene-A4 hydrolase |
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-Non-polymers , 5 types, 399 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-YB / |
#4: Chemical | ChemComp-PH0 / |
#5: Chemical | ChemComp-ACY / |
#6: 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: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion Details: Co-crystallized with LTA4H by liquid-liquid diffusion in melting-point capillaries. A Tris-buffered (10 mM, pH 7.5) solution of protein and inhibitor in approximately equimolar ...Details: Co-crystallized with LTA4H by liquid-liquid diffusion in melting-point capillaries. A Tris-buffered (10 mM, pH 7.5) solution of protein and inhibitor in approximately equimolar concentrations (~70 microM) was layered on the precipitate solution containing 28% (weight/volume) polyethylene glycol (Mw 8000), 50 mM Na acetate, 100 mM imidazole, pH 6.8, and 5 mM YbCl3, LIQUID DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→65.515 Å / Num. all: 53141 / Num. obs: 53141 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.89→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / Num. measured all: 42392 / Num. unique all: 7434 / Rsym value: 0.26 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Starting model: pdb entry1H19 Resolution: 1.89→14.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.944 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 28.108 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→14.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.944 Å / Total num. of bins used: 20
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