[English] 日本語
Yorodumi- PDB-2vw5: Structure Of The Hsp90 Inhibitor 7-O-carbamoylpremacbecin Bound T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vw5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure Of The Hsp90 Inhibitor 7-O-carbamoylpremacbecin Bound To The N- Terminus Of Yeast Hsp90 | ||||||
Components | ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 | ||||||
Keywords | CHAPERONE / ATPASE / CYTOPLASM / INHIBITOR / ATP-BINDING / STRESS RESPONSE / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / Neutrophil degranulation / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Roe, S.M. / Prodromou, C. / Pearl, L.H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Optimizing Natural Products by Biosynthetic Engineering: Discovery of Nonquinone Hsp90 Inhibitors. Authors: Zhang, M.Q. / Gaisser, S. / Nur-E-Alam, M. / Sheehan, L.S. / Vousden, W.A. / Gaitatzis, N. / Peck, G. / Coates, N.J. / Moss, S.J. / Radzom, M. / Foster, T.A. / Sheridan, R.M. / Gregory, M.A. ...Authors: Zhang, M.Q. / Gaisser, S. / Nur-E-Alam, M. / Sheehan, L.S. / Vousden, W.A. / Gaitatzis, N. / Peck, G. / Coates, N.J. / Moss, S.J. / Radzom, M. / Foster, T.A. / Sheridan, R.M. / Gregory, M.A. / Roe, S.M. / Prodromou, C. / Pearl, L.H. / Boyd, S.M. / Wilkinson, B. / Martin, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vw5.cif.gz | 348.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vw5.ent.gz | 287.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vw5_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2vw5_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2vw5_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 2vw5_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vw5 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vw5 | HTTPS FTP |
-Related structure data
Related structure data | 1amwS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
|
-Components
#1: Protein | Mass: 24208.582 Da / Num. of mol.: 4 / Fragment: N-TERM DOMAIN, RESIDUES 1-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PRSETA / References: UniProt: P02829 #2: Chemical | ChemComp-BC6 / ( #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.4 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→150 Å / Num. obs: 106928 / % possible obs: 92 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.38 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.77→1.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 0.9 / % possible all: 55.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AMW Resolution: 1.9→109.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.566 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 28.37 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→109.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|