[English] 日本語
![](img/lk-miru.gif)
- PDB-2w8y: RU486 bound to the progesterone receptor in a destabilized agonis... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2w8y | ||||||
---|---|---|---|---|---|---|---|
Title | RU486 bound to the progesterone receptor in a destabilized agonistic conformation | ||||||
![]() | PROGESTERONE RECEPTOR![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Raaijmakers, H.C.A. / Versteeg, J. / Uitdehaag, J.C.M. | ||||||
![]() | ![]() Title: The X-Ray Structure of Ru486 Bound to the Progesterone Receptor in a Destabilized Agonistic Conformation. Authors: Raaijmakers, H.C.A. / Versteegh, J. / Uitdehaag, J.C.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 118.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 29968.098 Da / Num. of mol.: 2 / Fragment: PR LBD, RESIDUES 678-933 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 204 molecules ![](data/chem/img/486.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NDR.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NDR.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-486 / ![]() |
---|---|
#3: Chemical | ChemComp-SO4 / ![]() |
#4: Chemical | ChemComp-NDR / (![]() |
#5: Chemical | ChemComp-EDO / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Details
Nonpolymer details | NORETHINDRONE (NDR): ALSO KNOWN AS NORETHISTERONE MIFEPRISTONE (486): RU486, 11BETA-4-N, N- ...NORETHINDR |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.46 % / Description: NONE |
---|---|
Crystal grow![]() | pH: 6.5 / Details: 22.5% PEG4000, 0.1M HEPES 6.5, 100 MM LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 17, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→47 Å / Num. obs: 45609 / % possible obs: 96.1 % / Observed criterion σ(I): -5 / Redundancy: 3.4 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.2 / % possible all: 77.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. THE DIMETHYLAMINOREMARK A909. IN REALITY WE PROBABLY OBSERVE THE AVERAGE OF AN ENSEMBLE OF SUBTLY DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. THE DIMETHYLAMINOREMARK A909. IN REALITY WE PROBABLY OBSERVE THE AVERAGE OF AN ENSEMBLE OF SUBTLY DIFFERENT DIMETHYLANILINE AND MET909 ORIENTATIONS, EACH STERICALLY ALLOWED. FOR THE FINAL REFINEMENT I SET THE OCCUPANCY OF M909 SIDECHAIN TO 0, TO IMPROVE THE FIT OF THE DIMETHYLANILINE TO THE ELECTRON DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 9.02 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→69.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|