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- PDB-5lt6: Structure of the Epigenetic Oncogene MMSET and inhibition by N-Al... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lt6 | ||||||
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Title | Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives | ||||||
![]() | Histone-lysine N-methyltransferase SETD2 | ||||||
![]() | TRANSFERASE / lysine methyltransferase SETD2 SET domain / SETD2#1 | ||||||
Function / homology | ![]() mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus ...mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus / pericardium development / stem cell development / nucleosome organization / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / response to type I interferon / positive regulation of ossification / embryonic cranial skeleton morphogenesis / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / alpha-tubulin binding / positive regulation of interferon-alpha production / mismatch repair / positive regulation of autophagy / forebrain development / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / neural tube closure / transcription elongation by RNA polymerase II / stem cell differentiation / response to organic cyclic compound / PKMTs methylate histone lysines / chromosome / regulation of gene expression / angiogenesis / defense response to virus / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tisi, D. / Pathuri, P. / Heightman, T. | ||||||
![]() | ![]() Title: Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives. Authors: Tisi, D. / Chiarparin, E. / Tamanini, E. / Pathuri, P. / Coyle, J.E. / Hold, A. / Holding, F.P. / Amin, N. / Martin, A.C. / Rich, S.J. / Berdini, V. / Yon, J. / Acklam, P. / Burke, R. / ...Authors: Tisi, D. / Chiarparin, E. / Tamanini, E. / Pathuri, P. / Coyle, J.E. / Hold, A. / Holding, F.P. / Amin, N. / Martin, A.C. / Rich, S.J. / Berdini, V. / Yon, J. / Acklam, P. / Burke, R. / Drouin, L. / Harmer, J.E. / Jeganathan, F. / van Montfort, R.L. / Newbatt, Y. / Tortorici, M. / Westlake, M. / Wood, A. / Hoelder, S. / Heightman, T.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.7 KB | Display | ![]() |
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PDB format | ![]() | 169.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lssC ![]() 5lsuC ![]() 5lsxC ![]() 5lsyC ![]() 5lszC ![]() 5lt7C ![]() 5lt8C 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34098.812 Da / Num. of mol.: 2 / Fragment: UNP residues 1433-1711 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9BYW2, histone-lysine N-methyltransferase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1MHepes,pH7.3, 0.1MKSCN, 25-30%MPEG2000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→61.86 Å / Num. obs: 98247 / % possible obs: 98.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 46.33 Å2 / Net I/σ(I): 6.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 59.623 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→61.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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