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- PDB-6ps9: Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ps9 | ||||||
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Title | Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 17 (5-{2-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]ethyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one) | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | PROTEIN BINDING / BRD4 BD1 / Bromodomain / Olinone | ||||||
Function / homology | ![]() 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 / chromatin / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ilyichova, O.V. / Scanlon, M.J. | ||||||
![]() | ![]() Title: Synthesis and elaboration of N-methylpyrrolidone as an acetamide fragment substitute in bromodomain inhibition. Authors: Hilton-Proctor, J.P. / Ilyichova, O. / Zheng, Z. / Jennings, I.G. / Johnstone, R.W. / Shortt, J. / Mountford, S.J. / Scanlon, M.J. / Thompson, P.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.7 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 333.6 KB | Display | ![]() |
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Full document | ![]() | 333.5 KB | Display | |
Data in XML | ![]() | 1.2 KB | Display | |
Data in CIF | ![]() | 4.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6prtC ![]() 6psbC ![]() 5dw2S 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
#1: Protein | Mass: 14968.182 Da / Num. of mol.: 1 / Fragment: UNP residues 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-Y17 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94645 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→44.14 Å / Num. obs: 40846 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 12.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1895 / CC1/2: 0.834 / Rpim(I) all: 0.391 / Rrim(I) all: 0.763 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5DW2 Resolution: 1.21→38.5 Å / SU ML: 0.1008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.9002
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→38.5 Å
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Refine LS restraints |
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LS refinement shell |
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