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Yorodumi- PDB-2vwc: STRUCTURE OF THE HSP90 INHIBITOR MACBECIN BOUND TO THE N-TERMINUS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vwc | |||||||||
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Title | STRUCTURE OF THE HSP90 INHIBITOR MACBECIN BOUND TO THE N-TERMINUS OF YEAST HSP90. | |||||||||
Components | ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 | |||||||||
Keywords | CHAPERONE / CHAPERONE-COMPLEX / INHIBITOR / HEAT SHOCK / ATP-BINDING / STRESS RESPONSE / MULTIGENE FAMILY / 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 / disordered domain specific binding / 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: 2.4 Å | |||||||||
Authors | Roe, S.M. / Prodromou, C. / Pearl, L.H. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Molecular Characterisation of Macbecin as an Hsp90 Inhibitor Authors: Martin, C.J. / Gaisser, S. / Challis, I.R. / Carletti, I. / Wilkinson, B. / Gregory, M. / Prodromou, C. / Roe, S.M. / Pearl, L.H. / Boyd, S.M. / Zhang, M.Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vwc.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vwc.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vwc_validation.pdf.gz | 878 KB | Display | wwPDB validaton report |
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Full document | 2vwc_full_validation.pdf.gz | 881.5 KB | Display | |
Data in XML | 2vwc_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 2vwc_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vwc ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vwc | HTTPS FTP |
-Related structure data
Related structure data | 1amwS S: Starting model for refinement |
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Similar 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: 24776.281 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829 |
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#2: Chemical | ChemComp-BC2 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.7 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.977 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 12582 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AMW Resolution: 2.4→73.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 12.542 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 32.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→73.72 Å
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