[English] 日本語

- PDB-4gl5: Structure of human placental aromatase complexed with designed in... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4gl5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human placental aromatase complexed with designed inhibitor HDDG029 (compound 4) | ||||||
![]() | Cytochrome P450 19A1 | ||||||
![]() | Oxidoreductase/Oxidoreductase Inhibitor / ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghosh, D. | ||||||
![]() | ![]() Title: Novel aromatase inhibitors by structure-guided design. Authors: Ghosh, D. / Lo, J. / Morton, D. / Valette, D. / Xi, J. / Griswold, J. / Hubbell, S. / Egbuta, C. / Jiang, W. / An, J. / Davies, H.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 756.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 769 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 57954.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HEM / ![]() |
#3: Chemical | ChemComp-G29 / ( |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.82 Å3/Da / Density % sol: 78.88 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion / pH: 7.4 Details: The enzyme-inhibitor complexes were prepared by the addition from 20mM stock solutions of compound 4 in PEG550 to 18 M (~1mg/ml) of aromatase, to give a final inhibitor concentration of 300 ...Details: The enzyme-inhibitor complexes were prepared by the addition from 20mM stock solutions of compound 4 in PEG550 to 18 M (~1mg/ml) of aromatase, to give a final inhibitor concentration of 300 uM. The mixture was incubated overnight at 4 C in 100mM potassium phosphate buffer pH 7.4 containing 20% glycerol, 20mM dithiothreitol, 0.5 M ASD and 1mM BDM. The complex was then concentrated to 25-30mg/ml using ultrafiltration. Protein was setup for crystallization using protein to cocktail ratios 2:1 and 3:1. The protein was mixed with reservoir cocktails of 24-30% polyethylene glycol 4000 in 50mM NaCl, 50mM Tris, pH 8.5 and vapor diffused in sealed 24-well sitting drop plates against corresponding reservoir solution., VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.48→121.53 Å / Num. all: 17289 / Num. obs: 17289 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 14.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.221 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.48→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.48→3.571 Å / Total num. of bins used: 20
|