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Yorodumi- PDB-3pgh: CYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2) COMPLEXED WITH A NON-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pgh | ||||||
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Title | CYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2) COMPLEXED WITH A NON-SELECTIVE INHIBITOR, FLURBIPROFEN | ||||||
Components | CYCLOOXYGENASE-2 | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / DIOXYGENASE / CYCLOOXYGENASE / NONSTEROIDAL ANTIINFLAMMATORY DRUGS / INFLAMMATION / ARTHRITIS / PROSTAGLANDIN / PROSTAGLANDIN SYNTHASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kurumbail, R. / Stallings, W. | ||||||
Citation | 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. #1: Journal: Nature / Year: 1997 Title: Erratum. 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pgh.cif.gz | 440.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pgh.ent.gz | 366 KB | Display | PDB format |
PDBx/mmJSON format | 3pgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pgh_validation.pdf.gz | 738 KB | Display | wwPDB validaton report |
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Full document | 3pgh_full_validation.pdf.gz | 835 KB | Display | |
Data in XML | 3pgh_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 3pgh_validation.cif.gz | 81.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/3pgh ftp://data.pdbj.org/pub/pdb/validation_reports/pg/3pgh | HTTPS FTP |
-Related structure data
Related structure data | 1cx2C 4coxC 5coxC 6coxC 1prhS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | Mass: 67318.719 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Tissue: DERMAL / Cell: FIBROBLAST / Cell line: CULTURED SF21 / Cellular location: ENDOPLASMIC RETICULUM / Cell line (production host): CULTURED SF21 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): OVARIAN TISSUE References: UniProt: Q05769, prostaglandin-endoperoxide synthase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-FLP / |
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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: 2.54 Å3/Da / Density % sol: 52 % / Description: PGHS-1 DIMER WAS USED AS THE SEARCH MODEL. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 20 MM SODIUM PHOSPHATE, 100 MM NACL, 0.6% BETA- OCTYLGLUCOSIDE, 10 MG/ML PROTEIN, 1MM INHIBITOR MIXED WITH A RESERVOIR SOLUTION CONTAINING 20-34% MONOMETHYL PEG 550, 10-240 MGCL2, 50 MM EPPS ...Details: 20 MM SODIUM PHOSPHATE, 100 MM NACL, 0.6% BETA- OCTYLGLUCOSIDE, 10 MG/ML PROTEIN, 1MM INHIBITOR MIXED WITH A RESERVOIR SOLUTION CONTAINING 20-34% MONOMETHYL PEG 550, 10-240 MGCL2, 50 MM EPPS PH 8.0 IN THE RATIO OF 1:1 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: SUPPER MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 76325 / % possible obs: 77.8 % / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.32 / Rsym value: 0.425 / % possible all: 65.4 |
Reflection | *PLUS Num. measured all: 2136154 |
Reflection shell | *PLUS % possible obs: 65.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROSTAGLANDIN SYNTHASE-1, PDB ENTRY 1PRH Resolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: AS IMPLEMENTED IN X-PLOR / σ(F): 2
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Displacement parameters | Biso mean: 15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.285 |