[English] 日本語
Yorodumi- PDB-1eqh: THE 2.7 ANGSTROM MODEL OF OVINE COX-1 COMPLEXED WITH FLURBIPROFEN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eqh | ||||||
---|---|---|---|---|---|---|---|
Title | THE 2.7 ANGSTROM MODEL OF OVINE COX-1 COMPLEXED WITH FLURBIPROFEN | ||||||
Components | PROSTAGLANDIN H2 SYNTHASE-1Cyclooxygenase | ||||||
Keywords | OXIDOREDUCTASE / EGF DOMAIN / NSAID Binding / Flurbiprofen / Membrane-Binding Domain / Cyclooxygenase / 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 / Resolution: 2.7 Å | ||||||
Authors | Loll, P.J. / Selinsky, B.S. / Gupta, K. / Sharkey, C.T. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1eqh.cif.gz | 244.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1eqh.ent.gz | 196.8 KB | Display | PDB format |
PDBx/mmJSON format | 1eqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eqh ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eqh | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer constructed from chain A and chain B, related by 2-fold NCS symmetry |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 66595.320 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 |
---|
-Sugars , 2 types, 13 molecules
#2: Sugar | ChemComp-NAG / #3: Sugar | |
---|
-Non-polymers , 3 types, 258 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.79 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 18K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4. ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→44.79 Å / Num. all: 62134 / Num. obs: 60445 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 2.7→2.87 Å / Rmerge(I) obs: 0.193 / Num. unique all: 8937 / % possible all: 94.4 |
Reflection | *PLUS Num. measured all: 273874 |
Reflection shell | *PLUS % possible obs: 93.8 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.7→44.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 267743.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.04 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.2 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44.79 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7.7 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.289 / % reflection Rfree: 7.6 % / Rfactor Rwork: 0.258 |