[English] 日本語
![](img/lk-miru.gif)
- PDB-3tda: Competitive replacement of thioridazine by prinomastat in crystal... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3tda | ||||||
---|---|---|---|---|---|---|---|
Title | Competitive replacement of thioridazine by prinomastat in crystals of cytochrome P450 2D6 | ||||||
![]() | Cytochrome P450 2D6 | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / monooxygenase / heme / prinomastat / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() negative regulation of binding / negative regulation of cellular organofluorine metabolic process / Miscellaneous substrates / isoquinoline alkaloid metabolic process / Fatty acids / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / arachidonate metabolic process / anandamide 8,9 epoxidase activity ...negative regulation of binding / negative regulation of cellular organofluorine metabolic process / Miscellaneous substrates / isoquinoline alkaloid metabolic process / Fatty acids / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / arachidonate metabolic process / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / alkaloid catabolic process / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / alkaloid metabolic process / 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 / long-chain fatty acid biosynthetic process / estrogen metabolic process / retinol metabolic process / Aspirin ADME / steroid metabolic process / xenobiotic catabolic process / monooxygenase activity / xenobiotic metabolic process / cholesterol metabolic process / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, A. / Stout, C.D. / Johnson, E.F. | ||||||
![]() | ![]() Title: Contributions of Ionic Interactions and Protein Dynamics to Cytochrome P450 2D6 (CYP2D6) Substrate and Inhibitor Binding. Authors: Wang, A. / Stout, C.D. / Zhang, Q. / Johnson, E.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 375 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 307.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3tbgC ![]() 4wntC ![]() 4wnuC ![]() 4wnvC ![]() 4wnwC ![]() 3qm4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 53730.566 Da / Num. of mol.: 4 / Fragment: UNP residues 34-497 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-PN0 / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.14 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG3350, sodium acetate, sodium cacodylate, potassium phosphate, sodium chloride, zinc chloride, glycerol, beta-mercaptoethanol, prinomastat, thioridazine, HEGA-10, facial amphiphile 231_ ...Details: PEG3350, sodium acetate, sodium cacodylate, potassium phosphate, sodium chloride, zinc chloride, glycerol, beta-mercaptoethanol, prinomastat, thioridazine, HEGA-10, facial amphiphile 231_CHOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, prinomastat was added after protein crystallization |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2011 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.668→42.186 Å / Num. all: 79050 / Num. obs: 79005 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 54.275 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.67→2.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.8 / Num. unique all: 11348 / Rsym value: 0.246 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QM4 Resolution: 2.67→42.04 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3017794.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.8196 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→42.04 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.67→2.84 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|