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- PDB-6bl3: Crystal Complex of Cyclooxygenase-2 with indomethacin-butyldiamin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bl3 | |||||||||
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Title | Crystal Complex of Cyclooxygenase-2 with indomethacin-butyldiamine-dansyl conjugate | |||||||||
![]() | Prostaglandin G/H synthase 2 | |||||||||
![]() | OXIDOREDUCTASE/INHIBITOR / cyclooxygenase-2 / fluorescent inhibitor complex / OXIDOREDUCTASE-INHIBITOR complex | |||||||||
Function / homology | ![]() 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 / prostaglandin secretion / response to vitamin D / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / prostaglandin biosynthetic process / nuclear inner membrane / 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 / decidualization / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / response to tumor necrosis factor / brown fat cell differentiation / response to glucocorticoid / keratinocyte differentiation / positive regulation of vasoconstriction / positive regulation of brown fat cell differentiation / embryo implantation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / memory / regulation of blood pressure / positive regulation of protein import into nucleus / peroxidase activity / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to estradiol / cellular response to heat / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / response to xenobiotic stimulus / neuron projection / positive regulation of apoptotic process / negative regulation of cell population proliferation / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xu, S. / Uddin, M.J. / Banerjee, S. / Marnett, L.J. | |||||||||
![]() | ![]() Title: Fluorescent indomethacin-dansyl conjugates utilize the membrane-binding domain of cyclooxygenase-2 to block the opening to the active site. Authors: Xu, S. / Uddin, M.J. / Banerjee, S. / Duggan, K. / Musee, J. / Kiefer, J.R. / Ghebreselasie, K. / Rouzer, C.A. / Marnett, L.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 923.2 KB | Display | ![]() |
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PDB format | ![]() | 767 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 88.4 KB | Display | |
Data in CIF | ![]() | 120.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bl4C ![]() 3nt1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 67332.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q05769, prostaglandin-endoperoxide synthase |
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-Sugars , 3 types, 18 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/BOG.gif)
![](data/chem/img/BOG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #6: Sugar | ChemComp-BOG / |
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-Non-polymers , 3 types, 864 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/L7M.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/L7M.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-L7M / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.08 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6.7 Details: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM ...Details: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM DMSO stocks were added to protein samples. Mixing 3 uL of the protein-inhibitor complex with 3 uL crystallization solution containing 50 mM EPPS, pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550 against reservoir solutions comprised of 50 mM EPPS pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.217→103.3 Å / Num. obs: 141148 / % possible obs: 97.83 % / Observed criterion σ(F): 1.34 / Redundancy: 3.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1535 / Rpim(I) all: 0.0977 / Rrim(I) all: 0.1826 / Net I/σ(I): 5.97 |
Reflection shell | Resolution: 2.217→2.296 Å / Rmerge(I) obs: 1.424 / Num. unique obs: 13090 / CC1/2: 0.458 / Rpim(I) all: 0.9065 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NT1 Resolution: 2.217→112.436 Å / SU ML: 0.3 / Phase error: 25.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.217→112.436 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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