[English] 日本語
![](img/lk-miru.gif)
- PDB-5o5f: Crystal structure of the human BRPF1 bromodomain in complex with BZ038 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5o5f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human BRPF1 bromodomain in complex with BZ038 | ||||||
![]() | Peregrin | ||||||
![]() | DNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription | ||||||
Function / homology | ![]() acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, J. / Caflisch, A. | ||||||
![]() | ![]() Title: Structure-based discovery of selective BRPF1 bromodomain inhibitors. Authors: Zhu, J. / Zhou, C. / Caflisch, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 70.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 749.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 751.6 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mwgC ![]() 5mwhC ![]() 5mwzC ![]() 5o4sC ![]() 5o4tC ![]() 5o55C ![]() 5o5aC ![]() 5o5hC ![]() 5ov8C ![]() 5owaC ![]() 6ekqC ![]() 4lc2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 13703.698 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-9LT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-tris propane, pH6.5, 0.2 M Sodium Nitrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→40.52 Å / Num. obs: 33637 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.022 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1591 / CC1/2: 0.802 / % possible all: 96.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 4LC2 Resolution: 1.302→30.382 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.64
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.302→30.382 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 27.6128 Å / Origin y: 1.7403 Å / Origin z: -9.6875 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |