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Yorodumi- PDB-1pge: PROSTAGLANDIN H2 SYNTHASE-1 COMPLEXED WITH P-(2'-IODO-5'-THENOYL)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pge | |||||||||
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Title | PROSTAGLANDIN H2 SYNTHASE-1 COMPLEXED WITH P-(2'-IODO-5'-THENOYL)HYDROTROPIC ACID (IODOSUPROFEN) | |||||||||
Components | PROSTAGLANDIN H2 SYNTHASE-1Cyclooxygenase | |||||||||
Keywords | OXIDOREDUCTASE / DIOXYGENASE / PEROXIDASE | |||||||||
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 / Resolution: 3.5 Å | |||||||||
Authors | Loll, P.J. / Picot, D. / Garavito, R.M. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Synthesis and use of iodinated nonsteroidal antiinflammatory drug analogs as crystallographic probes of the prostaglandin H2 synthase cyclooxygenase active site. Authors: Loll, P.J. / Picot, D. / Ekabo, O. / Garavito, R.M. #1: Journal: Nat.Struct.Biol. / Year: 1995 Title: The Structural Basis of Aspirin Activity Inferred from the Crystal Structure of Inactivated Prostaglandin H2 Synthase Authors: Loll, P.J. / Picot, D. / Garavito, R.M. #2: Journal: Nature / Year: 1994 Title: The X-Ray Crystal Structure of the Membrane Protein Prostaglandin H2 Synthase-1 Authors: Picot, D. / Loll, P.J. / Garavito, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pge.cif.gz | 230.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pge.ent.gz | 191.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/1pge ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pge | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.995479, -0.058108, 0.07513), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 66164.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organelle: SEMINAL VESICLESeminal vesicles References: PIR: A29947, UniProt: P05979*PLUS, prostaglandin-endoperoxide synthase |
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-Sugars , 3 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Sugar | |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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-Details
Sequence details | THIS SEQUENCE IS FOUND IN ENTRY 1PRH. THE NUMBERING IS DERIVED FROM THE PRE-PROTEIN, WHICH CONTAINS ...THIS SEQUENCE IS FOUND IN ENTRY 1PRH. THE NUMBERING IS DERIVED FROM THE PRE-PROTEIN, WHICH CONTAINS A 24-RESIDUE SIGNAL SEQUENCE WHICH IS CLEAVED DURING MATURATION |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Apr 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 28057 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.104 |
Reflection | *PLUS % possible obs: 90.9 % / Num. measured all: 69965 |
-Processing
Software |
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Refinement | Resolution: 3.5→15 Å / σ(F): 1 Details: THE STARTING MODEL FOR THIS REFINEMENT WAS THE 3.1 ANGSTROM REFINED CRYSTAL STRUCTURE OF THE PROSTAGLANDIN SYNTHASE-FLURBIPROFEN COMPLEX, FOR WHICH INDIVIDUAL ISOTROPIC ATOMIC TEMPERATURE ...Details: THE STARTING MODEL FOR THIS REFINEMENT WAS THE 3.1 ANGSTROM REFINED CRYSTAL STRUCTURE OF THE PROSTAGLANDIN SYNTHASE-FLURBIPROFEN COMPLEX, FOR WHICH INDIVIDUAL ISOTROPIC ATOMIC TEMPERATURE FACTORS WERE REFINED. THESE B-VALUES WERE USED FOR THIS STRUCTURE WITHOUT FURTHER REFINEMENT.
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Displacement parameters | Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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