[English] 日本語
Yorodumi- PDB-6c6p: Human squalene epoxidase (SQLE, squalene monooxygenase) structure... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c6p | ||||||
---|---|---|---|---|---|---|---|
Title | Human squalene epoxidase (SQLE, squalene monooxygenase) structure with FAD and NB-598 | ||||||
Components | Squalene monooxygenase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Cholesterol Synthesis Pathway / SQLE / ERG1 / FAD-dependent Monooxygenase / Squalene hydroxylase / Squalene-2 / 3-epoxidase / FLAVOPROTEIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information squalene monooxygenase / squalene monooxygenase activity / lipid droplet formation / sterol biosynthetic process / Cholesterol biosynthesis / ergosterol biosynthetic process / cholesterol metabolic process / FAD binding / : / Activation of gene expression by SREBF (SREBP) ...squalene monooxygenase / squalene monooxygenase activity / lipid droplet formation / sterol biosynthetic process / Cholesterol biosynthesis / ergosterol biosynthetic process / cholesterol metabolic process / FAD binding / : / Activation of gene expression by SREBF (SREBP) / regulation of cell population proliferation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Padyana, A.K. / Jin, L. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structure and inhibition mechanism of the catalytic domain of human squalene epoxidase. Authors: Padyana, A.K. / Gross, S. / Jin, L. / Cianchetta, G. / Narayanaswamy, R. / Wang, F. / Wang, R. / Fang, C. / Lv, X. / Biller, S.A. / Dang, L. / Mahoney, C.E. / Nagaraja, N. / Pirman, D. / ...Authors: Padyana, A.K. / Gross, S. / Jin, L. / Cianchetta, G. / Narayanaswamy, R. / Wang, F. / Wang, R. / Fang, C. / Lv, X. / Biller, S.A. / Dang, L. / Mahoney, C.E. / Nagaraja, N. / Pirman, D. / Sui, Z. / Popovici-Muller, J. / Smolen, G.A. #1: Journal: To be published Title: A chemical biology screen identifies a vulnerability of neuroendocrine cancer cells to SQLE inhibition. Authors: Mahoney, C. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E. / Chen, Y. / Huang, L. / Liu, M. / Zhang, Y. / McDonald, G. / Narayanaswamy, R. / Choe, S. / Chen, Y. ...Authors: Mahoney, C. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E. / Chen, Y. / Huang, L. / Liu, M. / Zhang, Y. / McDonald, G. / Narayanaswamy, R. / Choe, S. / Chen, Y. / Gross, S. / Cianchetta, G. / Padyana, A.K. / Murray, S. / Liu, W. / Marks, K. / Murtie, J. / Dorsch, M. / Jin, S. / Nagaraja, N. / Biller, S.A. / Roddy, T. / Popovici-Muller, J. / Smolen, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6c6p.cif.gz | 203.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6c6p.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 6c6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c6p_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6c6p_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6c6p_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 6c6p_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/6c6p ftp://data.pdbj.org/pub/pdb/validation_reports/c6/6c6p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 50895.770 Da / Num. of mol.: 2 / Fragment: residues 118-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SQLE, ERG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14534, squalene monooxygenase #2: Chemical | ChemComp-CPS / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.46 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M Ammonium sulfate, 0.1 M tri-Sodium citrate pH 5.6, 15 %(w/v) PEG 4000, 0.02 M Hexammine cobalt(III) chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-cooled double flat crystal Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→110.73 Å / Num. obs: 48368 / % possible obs: 88.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Χ2: 0.973 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→40.57 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.4
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|