+Open data
-Basic information
Entry | Database: PDB / ID: 2xx5 | ||||||
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Title | Macrolactone Inhibitor bound to HSP90 N-term | ||||||
Components | ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 | ||||||
Keywords | CHAPERONE | ||||||
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: 2 Å | ||||||
Authors | Moody, C.J. / Prodromou, C. / Pearl, L.H. / Roe, S.M. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2011 Title: Targeting the Hsp90 Molecular Chaperone with Novel Macrolactams. Synthesis, Structural, Binding, and Cellular Studies. Authors: Day, J.E. / Sharp, S.Y. / Rowlands, M.G. / Aherne, W. / Hayes, A. / Raynaud, F.I. / Lewis, W. / Roe, S.M. / Prodromou, C. / Pearl, L.H. / Workman, P. / Moody, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xx5.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xx5.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xx5_validation.pdf.gz | 878.2 KB | Display | wwPDB validaton report |
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Full document | 2xx5_full_validation.pdf.gz | 882.5 KB | Display | |
Data in XML | 2xx5_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2xx5_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/2xx5 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xx5 | HTTPS FTP |
-Related structure data
Related structure data | 2xx2C 2xx4C 1ah6S S: Starting model for refinement C: citing same article (ref.) |
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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: 24208.582 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 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) / References: UniProt: P02829 |
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#2: Chemical | ChemComp-13N / ( |
#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: 3.06 Å3/Da / Density % sol: 59.8 % / 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: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→38 Å / Num. obs: 21824 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AH6 Resolution: 2→37.989 Å / SU ML: 0.29 / σ(F): 0.98 / Phase error: 25.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.329 Å2 / ksol: 0.366 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→37.989 Å
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Refine LS restraints |
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LS refinement shell |
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