+Open data
-Basic information
Entry | Database: PDB / ID: 6hpx | ||||||
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Title | Crystal structure of ENL (MLLT1) in complex with compound 19 | ||||||
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 / lysine-acetylated histone binding / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / 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: 2.3 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 | 6hpx.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hpx.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 6hpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hpx_validation.pdf.gz | 648.7 KB | Display | wwPDB validaton report |
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Full document | 6hpx_full_validation.pdf.gz | 650 KB | Display | |
Data in XML | 6hpx_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 6hpx_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hpx ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hpx | HTTPS FTP |
-Related structure data
Related structure data | 6hpwC 6hpyC 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 | ChemComp-EDO / #3: Chemical | ChemComp-GKQ / ~{ | #4: 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: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% medium molecular weight PEG smears, 0.1M citrate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.8 Å / Num. obs: 7846 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 35.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.169 / Num. unique obs: 719 / CC1/2: 0.982 / Rpim(I) all: 0.083 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5j9s Resolution: 2.3→45.61 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.878 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.252 / 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: 38.457 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→45.61 Å
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Refine LS restraints |
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