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- PDB-3chp: Crystal structure of leukotriene a4 hydrolase in complex with (3S... -
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Basic information
Entry | Database: PDB / ID: 3chp | |||||||||
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Title | Crystal structure of leukotriene a4 hydrolase in complex with (3S)-3-amino-4-oxo-4-[(4-phenylmethoxyphenyl)amino]butanoic acid | |||||||||
![]() | Leukotriene A-4 hydrolase | |||||||||
![]() | HYDROLASE / EPOXIDE HYDROLASE / ALPHA-BETA PROTEIN / LEUKOTRIENE BIOSYNTHESIS / METALLOPROTEASE / Inhibitor complex / Alternative splicing / Cytoplasm / Metal-binding / Multifunctional enzyme / Zinc | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Thunnissen, M.M.G.M. / Adler, M. / Whitlow, M. | |||||||||
![]() | ![]() Title: Synthesis of glutamic acid analogs as potent inhibitors of leukotriene A4 hydrolase. Authors: Kirkland, T.A. / Adler, M. / Bauman, J.G. / Chen, M. / Haeggstrom, J.Z. / King, B. / Kochanny, M.J. / Liang, A.M. / Mendoza, L. / Phillips, G.B. / Thunnissen, M. / Trinh, L. / Whitlow, M. / ...Authors: Kirkland, T.A. / Adler, M. / Bauman, J.G. / Chen, M. / Haeggstrom, J.Z. / King, B. / Kochanny, M.J. / Liang, A.M. / Mendoza, L. / Phillips, G.B. / Thunnissen, M. / Trinh, L. / Whitlow, M. / Ye, B. / Ye, H. / Parkinson, J. / Guilford, W.J. #1: ![]() Title: Crystal Structure of Human Leukotriene A4 Hydrolase, a Bifunctional Enzyme in Inflammation Authors: Thunnissen, M.M.G.M. / Nordlund, P.N. / Haeggstrom, J.Z. #2: ![]() Title: Crystal structures of LEUKOTRIENE A4 HYDROLASE in complex with captopril and two competitive tight-binding inhibitors. Authors: Thunnissen, M.M.G.M. / Anderson, B. / Samuelsson, B. / Wong, C.-H. / Haeggstrom, J.Z. #3: ![]() 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. #4: ![]() Title: Leukotriene A4 Hydrolase: Identification of a Common Carboxylate Recognition Site for the Epoxide Hydrolase and Aminopeptidase Substrates Authors: Rudberg, P.C. / Tholander, F.O.T. / Andberg, M. / Thunnissen, M.M.G.M. / 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 | ![]() | 139.8 KB | Display | ![]() |
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PDB format | ![]() | 108.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69232.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 241 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/4BO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/YB.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/4BO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-YB / |
#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-IMD / |
#6: Chemical | ChemComp-4BO / ( |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 8 Details: PEG 8000, SODIUM ACETATE, IMIDEAZOLE PH 6.8, YBCL2, BESTATIN, LIQUID DIFFUSION, TEMPERATURE 298K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→26.09 Å / Num. obs: 45016 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5734 / Rsym value: 0.296 / % possible all: 99.6 |
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Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.1→24.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2018787.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: THERE IS POSITIVE FO-FC DENSITY BETWEEN THE ZN ION AND THE CARBOXYL OF THE INHIBITOR, AND AT THE 3 POSITION OF THE PHENYL-METHYL AT THE OTHER END OF THE INHIBITOR.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.3595 Å2 / ksol: 0.342296 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.85 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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