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- PDB-2ydw: Crystal Structure of the First Bromodomain of Human Brd2 with the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ydw | ||||||
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Title | Crystal Structure of the First Bromodomain of Human Brd2 with the inhibitor GW841819X | ||||||
![]() | BROMODOMAIN-CONTAINING PROTEIN 2 | ||||||
![]() | NUCLEAR PROTEIN / 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. / Delves, C. / Woodward, R. / Mirguet, O. / Nicodeme, E. | ||||||
![]() | ![]() Title: Discovery and Characterization of Small Molecule Inhibitors of the Bet Family Bromodomains. Authors: Chung, C.W. / Coste, H. / White, J.H. / Mirguet, O. / Wilde, J. / Gosmini, R.L. / Delves, C. / Magny, S.M. / Woodward, R. / Hughes, S.A. / Boursier, E.V. / Flynn, H. / Bouillot, A.M. / ...Authors: Chung, C.W. / Coste, H. / White, J.H. / Mirguet, O. / Wilde, J. / Gosmini, R.L. / Delves, C. / Magny, S.M. / Woodward, R. / Hughes, S.A. / Boursier, E.V. / Flynn, H. / Bouillot, A.M. / Bamborough, P. / Brusq, J.M. / Gellibert, F.J. / Jones, E.J. / Riou, A.M. / Homes, P. / Martin, S.L. / Uings, I.J. / Toum, J. / Clement, C.A. / Boullay, A.B. / Grimley, R.L. / Blandel, F.M. / Prinjha, R.K. / Lee, K. / Kirilovsky, J. / Nicodeme, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.3 KB | Display | ![]() |
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PDB format | ![]() | 122.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yekC ![]() 2yelC ![]() 2yemC ![]() 1e6iS S: Starting model for refinement 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 on special symmetry positions |
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Components
#1: Protein | Mass: 17779.547 Da / Num. of mol.: 3 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 67-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 42.2 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 17.5% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M BIS TRIS PH 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Date: Jun 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→67.26 Å / Num. obs: 34166 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E6I Resolution: 1.9→67.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.3 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.229 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→67.27 Å
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Refine LS restraints |
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