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- PDB-4dpr: Structure of human Leukotriene A4 hydrolase in complex with inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dpr | ||||||
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Title | Structure of human Leukotriene A4 hydrolase in complex with inhibitor captopril | ||||||
![]() | Leukotriene A-4 hydrolase | ||||||
![]() | hydrolase/hydrolase inhibitor / Leukotriene A4 / Metalloprotein / Protease / Zinc binding / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() leukotriene-A4 hydrolase / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase 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 / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stsiapanava, A. / Haeggstrom, J.Z. / Rinaldo-Matthis, A. | ||||||
![]() | ![]() Title: Capturing LTA4hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4synthesis. Authors: Stsiapanava, A. / Samuelsson, B. / Haeggstrom, J.Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.9 KB | Display | ![]() |
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PDB format | ![]() | 115.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477 KB | Display | ![]() |
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Full document | ![]() | 485.2 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ni2C ![]() 5ni4C ![]() 5ni6C ![]() 5niaC ![]() 5nidC ![]() 5nieC ![]() 1sqmS 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, 424 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/X8Z.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/X8Z.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-X8Z / | ||||||
#4: Chemical | ChemComp-YB / #5: Chemical | ChemComp-ACY / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 277 K / Method: liquid diffusion / pH: 6.7 Details: 26% PEG 8000, 0.1 mM Na-acetate, 0.1 mM Imidazole, 5 mM YbCL3, pH 6.7, LIQUID DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2011 |
Radiation | Monochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→65.69 Å / Num. all: 45143 / Num. obs: 45143 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.02→2.13 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SQM Resolution: 2.02→65.69 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.024 / SU ML: 0.11 / Isotropic thermal model: Isotopic / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.168 / 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: 15.805 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→65.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.072 Å / Total num. of bins used: 20
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