+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pq2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8 | ||||||
![]() | Cytochrome P450 2C8 | ||||||
![]() | OXIDOREDUCTASE / CYTOCHROME P450 / CYP2C8 / MEMBRANE PROTEIN / TAXOL 6-HYDROXYLASE | ||||||
Function / homology | ![]() omega-hydroxylase P450 pathway / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / organic acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity ...omega-hydroxylase P450 pathway / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / organic acid metabolic process / CYP2E1 reactions / arachidonate epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / Biosynthesis of maresin-like SPMs / oxidative demethylation / Xenobiotics / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / retinoic acid metabolic process / retinol metabolic process / estrogen metabolic process / long-chain fatty acid biosynthetic process / unspecific monooxygenase / Aspirin ADME / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schoch, G.A. / Yano, J.K. / Wester, M.R. / Griffin, K.J. / Stout, C.D. / Johnson, E.F. | ||||||
![]() | ![]() Title: Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site Authors: Schoch, G.A. / Yano, J.K. / Wester, M.R. / Griffin, K.J. / Stout, C.D. / Johnson, E.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 196.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 156.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n6bS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54054.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.36 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ETHANOL, PEG 4000, HEPES, SODIUM CHLORIDE, CYMAL-6 , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.6 Å / Num. all: 82164 / Num. obs: 38682 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rsym value: 0.052 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.3 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 50 Å / Num. obs: 34573 / % possible obs: 97.5 % / Num. measured all: 79013 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 97.9 % / Rmerge(I) obs: 0.512 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N6B Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.247 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|