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- PDB-7enz: Crystal structure of Phenanthredinone moiety in complex with the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7enz | ||||||
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Title | Crystal structure of Phenanthredinone moiety in complex with the second bromodomain of BRD2 (BRD2-BD2). | ||||||
![]() | Bromodomain-containing protein 2 | ||||||
![]() | TRANSCRIPTION / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor | ||||||
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 | ![]() ![]() | ||||||
![]() | Padmanabhan, B. / Arole, A. / Deshmukh, P. / Ashok, S. | ||||||
![]() | ![]() Title: Structural investigation of a pyrano-1,3-oxazine derivative and the phenanthridinone core moiety against BRD2 bromodomains. Authors: Arole, A.H. / Deshmukh, P. / Sridhar, A. / Padmanabhan, B. #1: ![]() Title: Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs. Authors: Mathur, S. / Deshmukh, P. / Tripathi, S. / Marimuthu, P. / Padmanabhan, B. #2: ![]() Title: Novel pyrano 1,3 oxazine based ligand inhibits the epigenetic reader hBRD2 in glioblastoma. Authors: Deshmukh, P. / Mathur, S. / Gangadharan, G. / Krishnappa, G. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46 KB | Display | ![]() |
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PDB format | ![]() | 29.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.5 KB | Display | ![]() |
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Full document | ![]() | 727.9 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7envC ![]() 7eo5C ![]() 5xhkS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13406.319 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 348-455 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-LDR / |
#3: Chemical | ChemComp-PGE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM Tris pH 7.5, 50 mM NaCl, 25% PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→14.1 Å / Num. obs: 13875 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 700 / CC1/2: 0.54 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XHK Resolution: 1.7→14.1 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→14.1 Å
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Refine LS restraints |
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LS refinement shell |
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