+Open data
-Basic information
Entry | Database: PDB / ID: 3q7d | ||||||
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Title | Structure of (R)-naproxen bound to mCOX-2. | ||||||
Components | Prostaglandin G/H synthase 2 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / PROSTAGLANDIN H2 SYNTHASE / CYCLOOXYGENASE-2 / NAPROXEN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / hair cycle / cellular response to homocysteine / Nicotinamide salvaging ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / hair cycle / cellular response to homocysteine / Nicotinamide salvaging / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / cellular response to lead ion / response to nematode / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of synaptic plasticity / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / response to fatty acid / response to fructose / positive regulation of fever generation / response to vitamin D / prostaglandin secretion / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / nuclear inner membrane / prostaglandin biosynthetic process / negative regulation of smooth muscle contraction / cellular response to ATP / positive regulation of cell migration involved in sprouting angiogenesis / maintenance of blood-brain barrier / bone mineralization / negative regulation of calcium ion transport / positive regulation of vasoconstriction / decidualization / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / response to tumor necrosis factor / positive regulation of synaptic transmission, glutamatergic / brown fat cell differentiation / response to glucocorticoid / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / learning / response to cytokine / caveola / regulation of blood pressure / peroxidase activity / cellular response to mechanical stimulus / memory / positive regulation of protein import into nucleus / positive regulation of peptidyl-serine phosphorylation / positive regulation of nitric oxide biosynthetic process / response to estradiol / cellular response to hypoxia / regulation of cell population proliferation / cellular response to heat / angiogenesis / response to oxidative stress / response to lipopolysaccharide / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / endoplasmic reticulum membrane / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Duggan, K.C. / Hermanson, D.J. / Musee, J. / Prusakiewicz, J.J. / Scheib, J. / Carter, B.D. / Banerjee, S. / Marnett, L.J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2011 Title: (R)-Profens are substrate-selective inhibitors of endocannabinoid oxygenation by COX-2. Authors: Duggan, K.C. / Hermanson, D.J. / Musee, J. / Prusakiewicz, J.J. / Scheib, J.L. / Carter, B.D. / Banerjee, S. / Oates, J.A. / Marnett, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q7d.cif.gz | 253.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q7d.ent.gz | 203 KB | Display | PDB format |
PDBx/mmJSON format | 3q7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q7d_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 3q7d_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3q7d_validation.xml.gz | 54.4 KB | Display | |
Data in CIF | 3q7d_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/3q7d ftp://data.pdbj.org/pub/pdb/validation_reports/q7/3q7d | HTTPS FTP |
-Related structure data
Related structure data | 3rr3C 3nt1S S: Starting model for refinement C: citing same article (ref.) |
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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, 2 molecules AB
#1: Protein | Mass: 67332.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q05769, prostaglandin-endoperoxide synthase |
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-Sugars , 2 types, 13 molecules
#2: Sugar | ChemComp-NAG / #5: Sugar | ChemComp-BOG / |
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-Non-polymers , 4 types, 604 molecules
#3: Chemical | #4: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.59 Å / Num. all: 65665 / Num. obs: 55701 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NT1 Resolution: 2.4→29.59 Å / SU ML: 0.29 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.018 Å2 / ksol: 0.303 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.59 Å
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Refine LS restraints |
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LS refinement shell |
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