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Yorodumi- PDB-1ht5: THE 2.75 ANGSTROM RESOLUTION MODEL OF OVINE COX-1 COMPLEXED WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ht5 | ||||||
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Title | THE 2.75 ANGSTROM RESOLUTION MODEL OF OVINE COX-1 COMPLEXED WITH METHYL ESTER FLURBIPROFEN | ||||||
Components | PROSTAGLANDIN H2 SYNTHASE-1Cyclooxygenase | ||||||
Keywords | OXIDOREDUCTASE / MEMBRANE PROTEIN / PEROXIDASE / DIOXYGENASE | ||||||
Function / homology | Function and homology information prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / intracellular membrane-bounded organelle / heme binding ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Selinsky, B.S. / Gupta, K. / Sharkey, C.T. / Loll, P.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural analysis of NSAID binding by prostaglandin H2 synthase: time-dependent and time-independent inhibitors elicit identical enzyme conformations. Authors: Selinsky, B.S. / Gupta, K. / Sharkey, C.T. / Loll, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ht5.cif.gz | 240 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ht5.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ht5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/1ht5 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/1ht5 | HTTPS FTP |
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-Related structure data
Related structure data | 1eqgC 1eqhC 1ht8C 1cqeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63511.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: SEMINAL VESICLESeminal vesicles References: UniProt: P05979, prostaglandin-endoperoxide synthase |
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-Sugars , 2 types, 13 molecules
#2: Sugar | #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 154 molecules
#4: Chemical | #5: Chemical | #6: 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: 4.54 Å3/Da / Density % sol: 72.92 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: PEG-4000, SODIUM CHLORIDE,BETA-OCTYL GLUCOSIDE, POTASSIUM PHOSPHATE (DIBASIC), pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: or 18 degrees centigrade | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 12, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50.89 Å / Num. all: 57793 / Num. obs: 53357 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.07 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.69 |
Reflection shell | Resolution: 2.75→2.92 Å / Redundancy: 4.07 % / Rmerge(I) obs: 0.189 / % possible all: 94.1 |
Reflection | *PLUS Num. measured all: 217384 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CQE Resolution: 2.75→50.89 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 338025.14 / Data cutoff low absF: 0 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.82 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→50.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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