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Yorodumi- PDB-6ddi: Crystal Structure of the human BRD2 BD1 bromodomain in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ddi | ||||||
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Title | Crystal Structure of the human BRD2 BD1 bromodomain in complex with a Tetrahydroquinoline analogue | ||||||
Components | Bromodomain-containing protein 2 | ||||||
Keywords | Transcription/Inhibitor / BET / BRD2 / bromodomain / Inhibitor / Complex / Transcription / Transcription-Inhibitor complex | ||||||
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 phosphorylation / 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: 1.5 Å | ||||||
Authors | White, S.W. / Yun, M. | ||||||
Citation | Journal: Cancer Res. / Year: 2020 Title: Bromodomain-Selective BET Inhibitors Are Potent Antitumor Agents against MYC-Driven Pediatric Cancer. Authors: Slavish, P.J. / Chi, L. / Yun, M.K. / Tsurkan, L. / Martinez, N.E. / Jonchere, B. / Chai, S.C. / Connelly, M. / Waddell, M.B. / Das, S. / Neale, G. / Li, Z. / Shadrick, W.R. / Olsen, R.R. / ...Authors: Slavish, P.J. / Chi, L. / Yun, M.K. / Tsurkan, L. / Martinez, N.E. / Jonchere, B. / Chai, S.C. / Connelly, M. / Waddell, M.B. / Das, S. / Neale, G. / Li, Z. / Shadrick, W.R. / Olsen, R.R. / Freeman, K.W. / Low, J.A. / Price, J.E. / Young, B.M. / Bharatham, N. / Boyd, V.A. / Yang, J. / Lee, R.E. / Morfouace, M. / Roussel, M.F. / Chen, T. / Savic, D. / Guy, R.K. / White, S.W. / Shelat, A.A. / Potter, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ddi.cif.gz | 161.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ddi.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ddi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ddi_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6ddi_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6ddi_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6ddi_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/6ddi ftp://data.pdbj.org/pub/pdb/validation_reports/dd/6ddi | HTTPS FTP |
-Related structure data
Related structure data | 6ddjC 4uyhS S: Starting model for refinement 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 on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 16150.830 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25440 |
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-Non-polymers , 5 types, 257 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Chemical | ChemComp-03S / | #6: 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: 2.26 Å3/Da / Density % sol: 45.56 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, ammonium sulfate, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.497→50 Å / Num. obs: 68247 / % possible obs: 98 % / Redundancy: 7 % / Biso Wilson estimate: 19.37 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Χ2: 1.442 / Net I/σ(I): 49.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UYH Resolution: 1.5→32.103 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.58 Å2 / Biso mean: 26.4191 Å2 / Biso min: 12.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→32.103 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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