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Yorodumi- PDB-4a9i: N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 3-methyl-1,2,3,4- tetra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a9i | ||||||
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Title | N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 3-methyl-1,2,3,4- tetrahydroquinazolin-2-one | ||||||
Components | BROMODOMAIN CONTAINING 2 | ||||||
Keywords | SIGNALING PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER | ||||||
Function / homology | Function and homology information 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 serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Chung, C.W. / Bamborough, P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Fragment-Based Discovery of Bromodomain Inhibitors Part 1: Inhibitor Binding Modes and Implications for Lead Discovery. Authors: Chung, C.W. / Dean, A.W. / Woolven, J.M. / Bamborough, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a9i.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a9i.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a9i_validation.pdf.gz | 492.7 KB | Display | wwPDB validaton report |
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Full document | 4a9i_full_validation.pdf.gz | 496.5 KB | Display | |
Data in XML | 4a9i_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 4a9i_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/4a9i ftp://data.pdbj.org/pub/pdb/validation_reports/a9/4a9i | HTTPS FTP |
-Related structure data
Related structure data | 4a9eC 4a9fC 4a9hC 4a9jC 4a9kC 4a9lC C: citing same article (ref.) |
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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: 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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25440 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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 Å3/Da / Density % sol: 38.48 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 0.1 M HEPES PH 7.0, 28% PEG 3350, 0.2 M (NH4)2SO4, 20 DEGREES CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. obs: 19710 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 96.6 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→68.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.921 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 46.824 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→68.04 Å
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Refine LS restraints |
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