[English] 日本語
Yorodumi- PDB-4dht: Small-molecule inhibitors of 14-3-3 protein-protein interactions ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dht | ||||||
---|---|---|---|---|---|---|---|
Title | Small-molecule inhibitors of 14-3-3 protein-protein interactions from virtual screening | ||||||
Components | 14-3-3 PROTEIN SIGMA | ||||||
Keywords | PROTEIN BINDING/INHIBITOR / HELICAL PROTEIN / ADAPTER PROTEIN / PHOSPHOPROTEIN BINDING / PROTEIN BINDING-INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Thiel, P. / Roeglin, L. / Kohlbacher, O. / Ottmann, C. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2013 Title: Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein-protein interactions. Authors: Thiel, P. / Roglin, L. / Meissner, N. / Hennig, S. / Kohlbacher, O. / Ottmann, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dht.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dht.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dht_validation.pdf.gz | 775.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4dht_full_validation.pdf.gz | 777.9 KB | Display | |
Data in XML | 4dht_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 4dht_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/4dht ftp://data.pdbj.org/pub/pdb/validation_reports/dh/4dht | HTTPS FTP |
-Related structure data
Related structure data | 3t0lC 3t0mC 4dhmC 4dhnC 4dhoC 4dhpC 4dhqC 4dhrC 4dhsC 4dhuC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26485.865 Da / Num. of mol.: 1 / Fragment: UNP resiudes 1-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, SFN / Plasmid: PPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA DE3 / References: UniProt: P31947 |
---|
-Non-polymers , 5 types, 297 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-0KG / { | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.93 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.095M HEPES Na, 0.19M calcium chloride, 5% glycerol, 28% PEG400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9778 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 20, 2011 Details: Sagittal - horizontal: Si(111) monochromator; Meridional - vertical: Dynamically bendable mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→45.52 Å / Num. all: 26906 / Num. obs: 26906 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.84 % / Biso Wilson estimate: 26.522 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.53 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 28.34 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.52 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2017 / WRfactor Rwork: 0.1589 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8782 / SU B: 2.256 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1147 / SU Rfree: 0.1154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.91 Å2 / Biso mean: 20.1926 Å2 / Biso min: 6.7 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.52 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|