[English] 日本語
Yorodumi- PDB-4e47: SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+47 | ||||||
---|---|---|---|---|---|---|---|
Title | SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine | ||||||
Components | Histone-lysine N-methyltransferase SETD7 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ternary complex / SET domain / methyltransferase / inhibitor / S-adenosylmethionine / chromatin regulator / chromosomal protein / nucleus / transcription / transcription regulation / transferase / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding / chromosome / chromatin organization / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Walker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. ...Walker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Setd7 in Complex with Inhibitor and SAM Authors: Walker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / ...Authors: Walker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4e47.cif.gz | 427.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4e47.ent.gz | 346.4 KB | Display | PDB format |
PDBx/mmJSON format | 4e47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/4e47 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/4e47 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3m53S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29683.951 Da / Num. of mol.: 4 / Fragment: SET domain (UNP residues 109-366) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: PHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 References: UniProt: Q8WTS6, histone-lysine N-methyltransferase |
---|
-Non-polymers , 5 types, 867 molecules
#2: Chemical | ChemComp-SAM / #3: Chemical | ChemComp-0N6 / ( #4: Chemical | ChemComp-BME / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 40% PEG3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 / Wavelength: 0.97932 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 72406 / Num. obs: 72406 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 28.51 Å2 / Rsym value: 0.097 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3345 / Rsym value: 0.627 / % possible all: 92.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3M53 Resolution: 2→39.88 Å / Cor.coef. Fo:Fc: 0.9572 / Cor.coef. Fo:Fc free: 0.9428 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.44 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.195 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.88 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|