+Open data
-Basic information
Entry | Database: PDB / ID: 6hpy | ||||||
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Title | Crystal structure of ENL (MLLT1) in complex with compound 12 | ||||||
Components | Protein ENL | ||||||
Keywords | TRANSCRIPTION / YEATS domain / inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Heidenreich, D. / Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2018 Title: Structure-Based Approach toward Identification of Inhibitory Fragments for Eleven-Nineteen-Leukemia Protein (ENL). Authors: Heidenreich, D. / Moustakim, M. / Schmidt, J. / Merk, D. / Brennan, P.E. / Fedorov, O. / Chaikuad, A. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hpy.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hpy.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hpy ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hpy | HTTPS FTP |
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-Related structure data
Related structure data | 6hpwC 6hpxC 6hpzC 6hq0C 5j9sS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18312.080 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q03111 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GKN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.2M ammonium sulfate, 0.1M bis-tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→66.39 Å / Num. obs: 11691 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 29.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.03 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 850 / CC1/2: 0.987 / Rpim(I) all: 0.08 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5j9s Resolution: 2→46 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.249 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.577 Å2
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Refinement step | Cycle: 1 / Resolution: 2→46 Å
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Refine LS restraints |
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