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- PDB-1igz: Crystal Structure of Linoleic acid Bound in the Cyclooxygenase Ch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1igz | |||||||||
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Title | Crystal Structure of Linoleic acid Bound in the Cyclooxygenase Channel of Prostaglandin Endoperoxide H Synthase-1. | |||||||||
![]() | Prostaglandin Endoperoxide H Synthase-1 | |||||||||
![]() | OXIDOREDUCTASE / membrane protein / fatty acid / linoleic acid / peroxidase / dioxygenase | |||||||||
Function / homology | ![]() prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Malkowski, M.G. / Thuresson, E.D. / Smith, W.L. / Garavito, R.M. | |||||||||
![]() | ![]() Title: Structure of eicosapentaenoic and linoleic acids in the cyclooxygenase site of prostaglandin endoperoxide H synthase-1. Authors: Malkowski, M.G. / Thuresson, E.D. / Lakkides, K.M. / Rieke, C.J. / Micielli, R. / Smith, W.L. / Garavito, R.M. #1: ![]() Title: Mutational and X-ray Crystallographic analysis of the Interaction of Dihomo-Gamma-Linolenic Acid with Prostaglandin Endoperoxide H Synthases. Authors: Thuresson, E.D. / Malkowski, M.G. / Lakkides, K.M. / Rieke, C.J. / Mulichak, A.M. / Ginell, S.L. / Garavito, R.M. / Smith, W.L. #2: ![]() Title: The Productive Conformation of Arachidonic Acid Bound to Prostaglandin Synthase. Authors: Malkowski, M.G. / Ginell, S.L. / Smith, W.L. / Garavito, R.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.8 KB | Display | ![]() |
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PDB format | ![]() | 96.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1igxC ![]() 1diyS 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 66164.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: GenBank: 165844, UniProt: P05979*PLUS, prostaglandin-endoperoxide synthase |
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-Sugars , 5 types, 6 molecules ![](data/chem/img/BGC.gif)
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#2: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: 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 |
#5: Sugar | ChemComp-BGC / |
#6: Sugar |
-Non-polymers , 3 types, 86 molecules ![](data/chem/img/COH.gif)
![](data/chem/img/EIC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EIC.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-COH / |
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#8: Chemical | ChemComp-EIC / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.15 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: lithium chloride, sodium azide, citric acid, n-octyl-glucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→15 Å / Num. all: 22730 / Num. obs: 22684 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
Reflection | *PLUS Num. obs: 21898 / % possible obs: 93 % |
Reflection shell | *PLUS % possible obs: 76 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1DIY Resolution: 2.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 4 % / Rfactor obs: 0.235 / Rfactor Rfree: 0.271 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Rfactor Rfree: 0.364 / Rfactor Rwork: 0.342 |