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Yorodumi- PDB-1cvu: CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND TO THE CYCLOOXYGENASE... -
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-Basic information
Entry | Database: PDB / ID: 1cvu | |||||||||
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Title | CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2 | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/peptide / COX-2 / CYCLOOXYGENASE / PROSTAGLANDIN / ARACHIDONATE / ENDOPEROXIDE / OXIDOREDUCTASE-peptide 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 / cellular response to homocysteine / 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 / cellular response to homocysteine / hair cycle / 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 / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / response to fatty acid / positive regulation of smooth muscle contraction / cyclooxygenase pathway / 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 / 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 / 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 / embryo implantation / positive regulation of brown fat cell differentiation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / positive regulation of smooth muscle cell proliferation / peroxidase activity / 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 / 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 / neuron projection / response to xenobiotic stimulus / 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | |||||||||
Authors | Kiefer, J.R. / Pawlitz, J.L. / Moreland, K.T. / Stegeman, R.A. / Gierse, J.K. / Stevens, A.M. / Goodwin, D.C. / Rowlinson, S.W. / Marnett, L.J. / Stallings, W.C. / Kurumbail, R.G. | |||||||||
Citation | 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. #1: Journal: Nature / Year: 1996 Title: Structural Basis for Selective Inhibition of by Anti-Inflammatory Agents Authors: Kurumbail, R.G. / Stevens, A.M. / 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cvu.cif.gz | 254.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cvu.ent.gz | 209.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/1cvu ftp://data.pdbj.org/pub/pdb/validation_reports/cv/1cvu | 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
-Protein / Protein/peptide , 2 types, 3 molecules ABF
#1: Protein | Mass: 63416.359 Da / Num. of mol.: 2 / Fragment: PROSTAGLANDIN H2 SYNTHASE-2 / Mutation: H207A (COX-1 NUMBERING) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PVL1393 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q05769, prostaglandin-endoperoxide synthase #2: Protein/peptide | | Mass: 907.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC |
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-Sugars , 4 types, 11 molecules
#3: Polysaccharide | #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | #6: Sugar | ChemComp-BOG / |
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-Non-polymers , 2 types, 773 molecules
#7: Chemical | #8: 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: 2.96 Å3/Da / Density % sol: 58.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MONOMETHYL PEG 550, MAGNESIUM SULFATE, ARACHIDNOIC ACID, EPPS, B-OG, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Details: Stevens, A.M., (1999) J. Cryst. Growth., 196, 350. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 8, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→35 Å / Num. all: 58608 / Num. obs: 212739 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.241 / % possible all: 97.8 |
Reflection | *PLUS Num. obs: 58608 / Num. measured all: 212739 |
-Processing
Software |
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Refinement | Resolution: 2.4→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: CONJUGATE GRADIENT, MOLECULAR DYNAMICS, INDIVIDUAL ATOM ISOTROPIC B, BULK SOLVENT CORRECTION
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Refinement step | Cycle: LAST / Resolution: 2.4→35 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |