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Yorodumi- PDB-7q5o: Bromodomain-containing 2 BD2 in complex with the inhibitor CRCM5484 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q5o | ||||||
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Title | Bromodomain-containing 2 BD2 in complex with the inhibitor CRCM5484 | ||||||
Components | Bromodomain-containing protein 2BRD2 | ||||||
Keywords | PROTEIN BINDING / Epigenetic / Inhibition / Inhibitor / Selectivity / Complex / BDII | ||||||
Function / homology | Function and homology information chromatin looping / acetylation-dependent protein binding / 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 ...chromatin looping / acetylation-dependent protein binding / 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: 1.519 Å | ||||||
Authors | Carrasco, K. / Betzi, S. / Morelli, X. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: CRCM5484: A BET-BDII Selective Compound with Differential Anti-leukemic Drug Modulation Authors: Carrasco, K. / Montersino, C. / Derviaux, C. / Saez-Ayala, M. / Hoffer, L. / Restouin, A. / Castellano, R. / Casassa, J. / Roche, P. / Pasquier, E. / Combes, S. / Morelli, X. / Collette, Y. / Betzi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q5o.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q5o.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 7q5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/7q5o ftp://data.pdbj.org/pub/pdb/validation_reports/q5/7q5o | HTTPS FTP |
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-Related structure data
Related structure data | 7q3fC 5xhkS C: citing same article (ref.) S: Starting model for refinement |
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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: 12926.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P25440 | ||||
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#2: Chemical | ChemComp-8M6 / | ||||
#3: Chemical | #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 |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 100 mM potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 275 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.885602 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.885602 Å / Relative weight: 1 |
Reflection | Resolution: 1.519→29.82 Å / Num. obs: 19199 / % possible obs: 98.26 % / Redundancy: 3.9 % / CC1/2: 0.927 / Rmerge(I) obs: 0.1796 / Rpim(I) all: 0.1012 / Rrim(I) all: 0.2075 / Net I/σ(I): 4.71 |
Reflection shell | Resolution: 1.52→1.574 Å / Rmerge(I) obs: 0.9046 / Num. unique obs: 1857 / CC1/2: 0.0807 / Rpim(I) all: 0.5353 / Rrim(I) all: 1.059 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XHK Resolution: 1.519→29.816 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.6 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.42 Å2 / Biso mean: 14.9459 Å2 / Biso min: 4.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.519→29.816 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 15.6232 Å / Origin y: 2.3221 Å / Origin z: 15.1009 Å
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Refinement TLS group | Selection details: chain 'A' and (resid 345 through 454 ) |