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Yorodumi- PDB-2yem: Crystal Structure of the Second Bromodomain of Human Brd4 with th... -
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-Basic information
Entry | Database: PDB / ID: 2yem | ||||||
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Title | Crystal Structure of the Second Bromodomain of Human Brd4 with the inhibitor GW841819X | ||||||
Components | BROMODOMAIN-CONTAINING PROTEIN 4 | ||||||
Keywords | SIGNALING PROTEIN / HISTONE / EPIGENETIC READER | ||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chung, C.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yem.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yem.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yem_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2yem_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2yem_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 2yem_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/2yem ftp://data.pdbj.org/pub/pdb/validation_reports/ye/2yem | HTTPS FTP |
-Related structure data
Related structure data | 2ydwC 2yekC 2yelC 1ouoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 15060.332 Da / Num. of mol.: 2 / Fragment: C-TERMINAL BROMODOMAIN, RESIDUES 333-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60885 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.8 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 2.5 M (NH4)2SO4, 0.1 M TRIS PH 8.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9765 |
Detector | Date: Sep 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→73.49 Å / Num. obs: 14749 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 36.96 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / % possible all: 98.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OUO Resolution: 2.3→52.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.062 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.205 / 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: 35.493 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→52.27 Å
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