+Open data
-Basic information
Entry | Database: PDB / ID: 4yk5 | ||||||
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Title | Crystal Structures of mPGES-1 Inhibitor Complexes | ||||||
Components | Prostaglandin E synthase | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / Inflammation / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process ...regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process / nuclear envelope lumen / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / sensory perception of pain / regulation of inflammatory response / cell population proliferation / negative regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å | ||||||
Authors | Luz, J.G. / Antonysamy, S. / Kuklish, S.L. / Fisher, M.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Crystal Structures of mPGES-1 Inhibitor Complexes Form a Basis for the Rational Design of Potent Analgesic and Anti-Inflammatory Therapeutics. Authors: Luz, J.G. / Antonysamy, S. / Kuklish, S.L. / Condon, B. / Lee, M.R. / Allison, D. / Yu, X.P. / Chandrasekhar, S. / Backer, R. / Zhang, A. / Russell, M. / Chang, S.S. / Harvey, A. / Sloan, A.V. / Fisher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yk5.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yk5.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/4yk5 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/4yk5 | HTTPS FTP |
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-Related structure data
-Links
-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: 17249.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGES, MGST1L1, MPGES1, PGES, PIG12 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14684, prostaglandin-E synthase |
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-Sugars , 2 types, 2 molecules
#5: Sugar | ChemComp-JZR / |
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#6: Sugar | ChemComp-BOG / |
-Non-polymers , 5 types, 150 molecules
#2: Chemical | ChemComp-4DV / |
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#3: Chemical | ChemComp-PG0 / |
#4: Chemical | ChemComp-GSH / |
#7: Chemical | ChemComp-PG4 / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.63 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris HCl pH 8.5 + 32.5% PEG 1K |
-Data collection
Diffraction | Mean temperature: 195 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 2, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→32 Å / Num. obs: 50979 / % possible obs: 99.3 % / Redundancy: 5.4 % / Net I/σ(I): 14.9 |
-Processing
Software |
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Refinement | Resolution: 1.42→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.274 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.042 / 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: 19.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→30 Å
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Refine LS restraints |
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