+Open data
-Basic information
Entry | Database: PDB / ID: 5tl9 | ||||||
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Title | crystal structure of mPGES-1 bound to inhibitor | ||||||
Components | Prostaglandin E synthase | ||||||
Keywords | Membrane Protein / Transferase / prostaglandin / enzyme / integral membrane protein / alpha helix / mPGES1 - ligand 0 | ||||||
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: 1.2 Å | ||||||
Authors | Luz, J.G. / Antonysamy, S. / Partridge, K. / Fisher, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2017 Title: Discovery and characterization of [(cyclopentyl)ethyl]benzoic acid inhibitors of microsomal prostaglandin E synthase-1. Authors: Partridge, K.M. / Antonysamy, S. / Bhattachar, S.N. / Chandrasekhar, S. / Fisher, M.J. / Fretland, A. / Gooding, K. / Harvey, A. / Hughes, N.E. / Kuklish, S.L. / Luz, J.G. / Manninen, P.R. / ...Authors: Partridge, K.M. / Antonysamy, S. / Bhattachar, S.N. / Chandrasekhar, S. / Fisher, M.J. / Fretland, A. / Gooding, K. / Harvey, A. / Hughes, N.E. / Kuklish, S.L. / Luz, J.G. / Manninen, P.R. / McGee, J.E. / Mudra, D.R. / Navarro, A. / Norman, B.H. / Quimby, S.J. / Schiffler, M.A. / Sloan, A.V. / Warshawsky, A.M. / Weller, J.M. / York, J.S. / Yu, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tl9.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tl9.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 5tl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/5tl9 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/5tl9 | 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: 17323.559 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
#4: Sugar | ChemComp-JZR / |
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#5: Sugar | ChemComp-BOG / |
-Non-polymers , 5 types, 142 molecules
#2: Chemical | ChemComp-7DN / | ||||
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#3: Chemical | ChemComp-GSH / | ||||
#6: Chemical | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 294.15 K / Method: vapor diffusion / Details: 0.1M TRIS pH 8.9 28% PEG 1K |
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-Data collection
Diffraction | Mean temperature: 78.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→19.54 Å / Num. obs: 80353 / % possible obs: 98.6 % / Redundancy: 5.4 % / Rsym value: 0.1 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.65 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Resolution: 1.2→19.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.963 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.267 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→19.54 Å
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Refine LS restraints |
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