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- PDB-4fmu: Crystal structure of Methyltransferase domain of human SET domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fmu | ||||||
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Title | Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF | ||||||
![]() | Histone-lysine N-methyltransferase SETD2 | ||||||
![]() | TRANSFERASE / Structural Genomics Consortium / SGC / Methyltransferase / SET domain-containing protein 2 / Pr-SNF | ||||||
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 / embryonic cranial skeleton morphogenesis / positive regulation of ossification / 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 / positive regulation of autophagy / mismatch repair / 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 | ![]() ![]() ![]() | ||||||
![]() | Dong, A. / Zeng, H. / Ibanez, G. / Zheng, W. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. ...Dong, A. / Zeng, H. / Ibanez, G. / Zheng, W. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Luo, M. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Sinefungin Derivatives as Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2. Authors: Zheng, W. / Ibanez, G. / Wu, H. / Blum, G. / Zeng, H. / Dong, A. / Li, F. / Hajian, T. / Allali-Hassani, A. / Amaya, M.F. / Siarheyeva, A. / Yu, W. / Brown, P.J. / Schapira, M. / Vedadi, M. / Min, J. / Luo, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.5 KB | Display | ![]() |
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PDB format | ![]() | 45.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.6 KB | Display | ![]() |
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Full document | ![]() | 777.7 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h12C ![]() 3h6l 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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Unit cell |
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Components
#1: Protein | Mass: 31955.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9BYW2, histone-lysine N-methyltransferase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-0UM / ( | #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG4000, 10% isoprpanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR 300 CCD / Detector: CCD / Date: Nov 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 19073 / Num. obs: 18501 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 38.63 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 42.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.08 / Num. unique all: 769 / Rsym value: 0.221 / % possible all: 82.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H6L ![]() 3h6l Resolution: 2.1→35.12 Å / Cor.coef. Fo:Fc: 0.9135 / Cor.coef. Fo:Fc free: 0.8853 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.262 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→35.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Total num. of bins used: 9
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