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Yorodumi- PDB-1pxx: CRYSTAL STRUCTURE OF DICLOFENAC BOUND TO THE CYCLOOXYGENASE ACTIV... -
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-Basic information
Entry | Database: PDB / ID: 1pxx | |||||||||
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Title | CRYSTAL STRUCTURE OF DICLOFENAC BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2 | |||||||||
Components | Prostaglandin G/H synthase 2Cyclooxygenase | |||||||||
Keywords | OXIDOREDUCTASE / COX-2 / CYCLOOXYGENASE / PROSTAGLANDIN / DICLOFENAC / ENDOPEROXIDE | |||||||||
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 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / 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 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / Nicotinamide salvaging / 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 / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / response to fructose / positive regulation of smooth muscle contraction / response to fatty acid / cyclooxygenase pathway / 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 / prostaglandin biosynthetic process / nuclear inner membrane / cellular response to ATP / negative regulation of smooth muscle contraction / maintenance of blood-brain barrier / positive regulation of cell migration involved in sprouting angiogenesis / 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 / positive regulation of vasoconstriction / response to glucocorticoid / keratinocyte differentiation / embryo implantation / positive regulation of brown fat cell differentiation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / peroxidase activity / 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 / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / response to estradiol / cellular response to heat / positive regulation of peptidyl-serine phosphorylation / regulation of cell population proliferation / cellular response to hypoxia / 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 / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å | |||||||||
Authors | Kiefer, J.R. / Rowlinson, S.W. / Prusakiewicz, J.J. / Pawlitz, J.L. / Kozak, K.R. / Kalgutkar, A.S. / Stallings, W.C. / Marnett, L.J. / Kurumbail, R.G. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: A Novel Mechanism of Cyclooxygenase-2 Inhibition Involving Interactions with Ser-530 and Tyr-385. Authors: Rowlinson, S.W. / Kiefer, J.R. / Prusakiewicz, J.J. / Pawlitz, J.L. / Kozak, K.R. / Kalgutkar, A.S. / Stallings, W.C. / Kurumbail, R.G. / Marnett, L.J. #1: Journal: Nature / Year: 1996 Title: Structural Basis for Selective Inhibition of cyclooxygenase-2 by Anti-Inflammatory Agents Authors: Kurumbail, R.G. / Stevens, A.M. / Gierse, J.K. / McDonald, J.J. / Stegeman, R.A. / Pak, J.Y. / Gildehaus, D. / Miyashiro, J.M. / Penning, T.D. / Seibert, K. / Isakson, P.C. / Stallings, W.C. #2: Journal: Nature / Year: 2000 Title: Structural insights into the stereochemistry of the cyclooxygenase reaction Authors: Kiefer, J.R. / Pawlitz, J.L. / Moreland, K.T. / Stegeman, R.A. / Hood, W.F. / Gierse, J.K. / Stevens, A.M. / Goodwin, D.C. / Rowlinson, S.W. / Marnett, L.J. / Stallings, W.C. / Kurumbail, R.G. | |||||||||
History |
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Remark 999 | SEQUENCE The first 17 residues are not observed in the electron density. The full sequence of the ...SEQUENCE The first 17 residues are not observed in the electron density. The full sequence of the sequence database reference was included in the SEQRES record. The C-terminal ~3KDa of the protein are cleaved off by trypsin. The authors have not determined the final C-terminal amino acid of the resulting protein and do not know the cleavage site. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pxx.cif.gz | 465.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pxx.ent.gz | 379.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/1pxx ftp://data.pdbj.org/pub/pdb/validation_reports/px/1pxx | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: 69092.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: PTGS2 OR COX2 OR COX-2 OR TIS10 OR PGHS-B / Plasmid: PVL1393 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q05769, prostaglandin-endoperoxide synthase |
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-Sugars , 3 types, 14 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose #3: Sugar | ChemComp-NAG / #4: Sugar | |
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-Non-polymers , 3 types, 325 molecules
#5: Chemical | ChemComp-HEM / #6: Chemical | ChemComp-DIF / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Monomethyl PEG 550, Magnesium Chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal grow | *PLUS Details: Gierse, J.K., (1995) Biochem. J., 305, 479. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 67852 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 5.3 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.161 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 6699 / Rsym value: 0.381 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 362090 / Rmerge(I) obs: 0.161 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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