[English] 日本語
![](img/lk-miru.gif)
- PDB-4ir4: Crystal Structure of the bromodomain of human BAZ2B in complex wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ir4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the bromodomain of human BAZ2B in complex with 1-[7-(morpholin-4-yl)-1-(pyridin-2-yl)indolizin-3-yl]ethanone (GSK2834113A) | ||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
![]() | TRANSCRIPTION / SGC / Structural Genomics Consortium / bromodomain / acetylated lysine binding protein / KIAA1476 / WALp4 | ||||||
Function / homology | ![]() chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chaikuad, A. / Felletar, I. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. ...Chaikuad, A. / Felletar, I. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Discovery and Characterization of GSK2801, a Selective Chemical Probe for the Bromodomains BAZ2A and BAZ2B. Authors: Chen, P. / Chaikuad, A. / Bamborough, P. / Bantscheff, M. / Bountra, C. / Chung, C.W. / Fedorov, O. / Grandi, P. / Jung, D. / Lesniak, R. / Lindon, M. / Muller, S. / Philpott, M. / Prinjha, ...Authors: Chen, P. / Chaikuad, A. / Bamborough, P. / Bantscheff, M. / Bountra, C. / Chung, C.W. / Fedorov, O. / Grandi, P. / Jung, D. / Lesniak, R. / Lindon, M. / Muller, S. / Philpott, M. / Prinjha, R. / Rogers, C. / Selenski, C. / Tallant, C. / Werner, T. / Willson, T.M. / Knapp, S. / Drewry, D.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 68.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 49.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 761.9 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ir3C ![]() 4ir5C ![]() 4ir6C ![]() 4rvrC ![]() 3g0lS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 13618.652 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-IR4 / | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IN THIS ENTRY CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.91 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: 32% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.25 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 3, 2011 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→19.68 Å / Num. all: 14789 / Num. obs: 14774 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2 / Num. unique all: 2097 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3G0L Resolution: 2.05→19.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.799 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.135 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.822 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.273 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→19.6 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|