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Yorodumi- PDB-4mkt: Human Leukotriene A4 Hydrolase in complex with Pro-Gly-Pro analog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mkt | ||||||
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Title | Human Leukotriene A4 Hydrolase in complex with Pro-Gly-Pro analogue and 4-(4-benzylphenyl)thiazol-2-amine | ||||||
Components | Leukotriene A-4 hydrolase | ||||||
Keywords | HYDROLASE / Leukotriene A4 Hydrolase / Metalloprotein / protease / Zinc binding | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.618 Å | ||||||
Authors | Stsiapanava, A. / Rinaldo-Matthis, A. / Haeggstrom, J.Z. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Binding of Pro-Gly-Pro at the active site of leukotriene A4 hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor. Authors: Stsiapanava, A. / Olsson, U. / Wan, M. / Kleinschmidt, T. / Rutishauser, D. / Zubarev, R.A. / Samuelsson, B. / Rinaldo-Matthis, A. / 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 | 4mkt.cif.gz | 161.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mkt.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mkt_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4mkt_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4mkt_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 4mkt_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/4mkt ftp://data.pdbj.org/pub/pdb/validation_reports/mk/4mkt | HTTPS FTP |
-Related structure data
Related structure data | 4l2lC 4ms6C 4dprS C: citing same article (ref.) S: Starting model for refinement |
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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: LTA4, LTA4H / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09960, leukotriene-A4 hydrolase |
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-Non-polymers , 6 types, 642 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-28T / | ||||
#4: Chemical | ChemComp-1V6 / | ||||
#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: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 277 K / Method: liquid diffusion / pH: 7 Details: 50 mM Sodium Acetate, 22% (v/v) PEG 8000, 5 mM YbCl3, pH 7.0, LIQUID DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2013 / Details: Mirrors |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.618→43.79 Å / Num. all: 86651 / Num. obs: 86391 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.61 % / Biso Wilson estimate: 26.45 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.51 |
Reflection shell | Resolution: 1.618→1.72 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.96 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DPR Resolution: 1.618→43.79 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.666 / SU ML: 0.057 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.086 / 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: 20.317 Å2
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Refinement step | Cycle: LAST / Resolution: 1.618→43.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.618→1.66 Å / Total num. of bins used: 20
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