+Open data
-Basic information
Entry | Database: PDB / ID: 7vs0 | ||||||
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Title | crystal structure of BRD2-BD2 in complex with purine derivative | ||||||
Components | Bromodomain-containing protein 2 | ||||||
Keywords | TRANSCRIPTION/INHIBITOR / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor / 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 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 / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Padmanabhan, B. / Arole, A. / Deshmukh, P. / Ashok, S. / Mathur, S. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family. Authors: Arole, A.H. / Deshmukh, P. / Sridhar, A. / Mathur, S. / Mahalingaswamy, M. / Subramanya, H. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vs0.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vs0.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vs0_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7vs0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7vs0_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 7vs0_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/7vs0 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/7vs0 | HTTPS FTP |
-Related structure data
Related structure data | 7vrhC 7vriC 7vrkC 7vrmC 7vroC 7vrqC 7vrzC 7vs1C 7vsfC 5xhkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 13524.474 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P25440 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: PEG MME 2000, 50mM Tris, 50mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 6, 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: 1.25→38.89 Å / Num. obs: 33667 / % possible obs: 98.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 11.04 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.88 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / Num. unique obs: 1545 / CC1/2: 0.96 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XHK Resolution: 1.25→35.89 Å / SU ML: 0.0922 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.7848 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→35.89 Å
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Refine LS restraints |
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LS refinement shell |
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