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- PDB-4a9h: N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-(2-methyl-1,2,3,4-tet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a9h | ||||||
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Title | N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-(2-methyl-1,2,3,4-tetrahydroquinolin-1-yl)ethan-1-one | ||||||
![]() | BROMODOMAIN-CONTAINING PROTEIN 2 | ||||||
![]() | SIGNALING PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER | ||||||
Function / homology | ![]() acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chung, C.W. / Bamborough, P. | ||||||
![]() | ![]() Title: Fragment-Based Discovery of Bromodomain Inhibitors Part 1: Inhibitor Binding Modes and Implications for Lead Discovery. Authors: Chung, C.W. / Dean, T.W. / Woolven, J.M. / Bamborough, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.8 KB | Display | ![]() |
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PDB format | ![]() | 127.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.2 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a9eC ![]() 4a9fC ![]() 4a9iC ![]() 4a9jC ![]() 4a9kC ![]() 4a9lC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17908.727 Da / Num. of mol.: 3 / Fragment: N-TERMINAL BROMODOMAIN (BD1), RESIDUES 67-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.82 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 8 Details: 0.1M HEPES, PH 8.0 30% PEG3350, 0.2M (NH4)2SO4, 20C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→67.88 Å / Num. obs: 26554 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.883 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→67.88 Å
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Refine LS restraints |
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