+Open data
-Basic information
Entry | Database: PDB / ID: 5kjm | ||||||
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Title | SMYD2 in complex with AZ931 | ||||||
Components | N-lysine methyltransferase SMYD2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANFERASE / histone methyltransferase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / PKMTs methylate histone lysines / Regulation of TP53 Activity through Methylation / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Ferguson, A. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2016 Title: Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. Authors: Cowen, S.D. / Russell, D. / Dakin, L.A. / Chen, H. / Larsen, N.A. / Godin, R. / Throner, S. / Zheng, X. / Molina, A. / Wu, J. / Cheung, T. / Howard, T. / Garcia-Arenas, R. / Keen, N. / ...Authors: Cowen, S.D. / Russell, D. / Dakin, L.A. / Chen, H. / Larsen, N.A. / Godin, R. / Throner, S. / Zheng, X. / Molina, A. / Wu, J. / Cheung, T. / Howard, T. / Garcia-Arenas, R. / Keen, N. / Pendleton, C.S. / Pietenpol, J.A. / Ferguson, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kjm.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kjm.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kjm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5kjm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5kjm_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 5kjm_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kjm ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kjm | HTTPS FTP |
-Related structure data
Related structure data | 5kjkC 5kjlC 5kjnC 3s7bS 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: 49343.582 Da / Num. of mol.: 1 / Mutation: G165E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Production host: Escherichia coli (E. coli) References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase | ||
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#2: Chemical | ChemComp-SAM / | ||
#3: Chemical | ChemComp-6TM / | ||
#4: Chemical | #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: 3.25 Å3/Da / Density % sol: 62.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350, 0.1 M Tris-HCl, 5% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→78.02 Å / Num. obs: 32761 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 43.59 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.19→2.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3s7b Resolution: 2.19→78.02 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.159
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Displacement parameters | Biso mean: 46.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→78.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Origin x: -51.4844 Å / Origin y: 20.7418 Å / Origin z: -0.898 Å
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Refinement TLS group | Selection details: { A|* } |