+Open data
-Basic information
Entry | Database: PDB / ID: 7lzf | ||||||
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Title | Crystal Structure of SETD2 bound to Compound 57 | ||||||
Components | Histone-lysine N-methyltransferase SETD2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | ||||||
Authors | Farrow, N.A. / Boriack-Sjodin, P. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: Discovery of a First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable for Preclinical Studies. Authors: Lampe, J.W. / Alford, J.S. / Boriak-Sjodin, P.A. / Brach, D. / Cosmopoulos, K. / Duncan, K.W. / Eckley, S.T. / Foley, M.A. / Harvey, D.M. / Motwani, V. / Munchhof, M.J. / Raimondi, A. / ...Authors: Lampe, J.W. / Alford, J.S. / Boriak-Sjodin, P.A. / Brach, D. / Cosmopoulos, K. / Duncan, K.W. / Eckley, S.T. / Foley, M.A. / Harvey, D.M. / Motwani, V. / Munchhof, M.J. / Raimondi, A. / Riera, T.V. / Tang, C. / Thomenius, M.J. / Totman, J. / Farrow, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lzf.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lzf.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 7lzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lzf_validation.pdf.gz | 1021.2 KB | Display | wwPDB validaton report |
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Full document | 7lzf_full_validation.pdf.gz | 1021.9 KB | Display | |
Data in XML | 7lzf_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 7lzf_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/7lzf ftp://data.pdbj.org/pub/pdb/validation_reports/lz/7lzf | HTTPS FTP |
-Related structure data
Related structure data | 7lzbC 7lzdC 5jleS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31955.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 / Production host: Baculovirus expression vector pFastBac1-HM References: UniProt: Q9BYW2, [histone H3]-lysine36 N-trimethyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 5 types, 43 molecules
#2: Chemical | #3: Chemical | ChemComp-SAM / | #4: Chemical | ChemComp-YHV / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953722 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953722 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→41.82 Å / Num. obs: 10278 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.47→2.57 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 715 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JLE Resolution: 2.47→36.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.8 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.535 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.84 Å2 / Biso mean: 62.722 Å2 / Biso min: 39.94 Å2
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Refinement step | Cycle: final / Resolution: 2.47→36.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.473→2.537 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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