+Open data
-Basic information
Entry | Database: PDB / ID: 5d3s | ||||||
---|---|---|---|---|---|---|---|
Title | First bromodomain of BRD4 bound to inhibitor XD44 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / Gene regulation / Bromodomain / Inhibitor | ||||||
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Wohlwend, D. / Huegle, M. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: 4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1). Authors: Hugle, M. / Lucas, X. / Weitzel, G. / Ostrovskyi, D. / Breit, B. / Gerhardt, S. / Einsle, O. / Gunther, S. / Wohlwend, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5d3s.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5d3s.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 5d3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d3s_validation.pdf.gz | 766.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5d3s_full_validation.pdf.gz | 767.6 KB | Display | |
Data in XML | 5d3s_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 5d3s_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/5d3s ftp://data.pdbj.org/pub/pdb/validation_reports/d3/5d3s | HTTPS FTP |
-Related structure data
Related structure data | 5d24C 5d25C 5d26C 5d3hC 5d3jC 5d3lC 5d3nC 5d3pC 5d3rC 5d3tC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15012.301 Da / Num. of mol.: 1 / Fragment: First bromodomain, UNP residues 44-168 / Mutation: T43M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 |
---|---|
#2: Chemical | ChemComp-579 / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-BU3 / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.61 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25 Å / Num. obs: 11878 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.75→1.84 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1690 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.054 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.441 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|