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Yorodumi- PDB-7o2c: X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o2c | ||||||
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Title | X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035 | ||||||
Components | Histone-lysine N-methyltransferase SMYD3 | ||||||
Keywords | TRANSFERASE / Smyd3 / methyl transferase | ||||||
Function / homology | Function and homology information histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / positive regulation of peptidyl-serine phosphorylation / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Steuber, H. | ||||||
Citation | Journal: Slas Discov / Year: 2021 Title: Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening. Authors: Gradl, S. / Steuber, H. / Weiske, J. / Szewczyk, M.M. / Schmees, N. / Siegel, S. / Stoeckigt, D. / Christ, C.D. / Li, F. / Organ, S. / Abbey, M. / Kennedy, S. / Chau, I. / Trush, V. / ...Authors: Gradl, S. / Steuber, H. / Weiske, J. / Szewczyk, M.M. / Schmees, N. / Siegel, S. / Stoeckigt, D. / Christ, C.D. / Li, F. / Organ, S. / Abbey, M. / Kennedy, S. / Chau, I. / Trush, V. / Barsyte-Lovejoy, D. / Brown, P.J. / Vedadi, M. / Arrowsmith, C. / Husemann, M. / Badock, V. / Bauser, M. / Haegebarth, A. / Hartung, I.V. / Stresemann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o2c.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o2c.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 7o2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o2c_validation.pdf.gz | 379.7 KB | Display | wwPDB validaton report |
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Full document | 7o2c_full_validation.pdf.gz | 384.3 KB | Display | |
Data in XML | 7o2c_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 7o2c_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/7o2c ftp://data.pdbj.org/pub/pdb/validation_reports/o2/7o2c | HTTPS FTP |
-Related 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: 49178.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H7B4, [histone H3]-lysine4 N-trimethyltransferase | ||||
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#2: Chemical | ChemComp-UZK / ( | ||||
#3: Chemical | ChemComp-SAM / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 8 % PEG 3350, 50 mM magnesium formate, 100 mM Tris pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→41.64 Å / Num. obs: 68061 / % possible obs: 99.5 % / Redundancy: 5.3 % / CC1/2: 0.997 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.52→1.61 Å / Num. unique obs: 10752 / CC1/2: 0.718 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: previously solved inhouse structure Resolution: 1.52→41.64 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.672 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.085 / 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: 91.36 Å2 / Biso mean: 18.237 Å2 / Biso min: 7 Å2
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Refinement step | Cycle: final / Resolution: 1.52→41.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.556 Å / Rfactor Rfree error: 0
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