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Yorodumi- PDB-7k9w: Cryptococcus neoformans Hsp90 nucleotide binding domain in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k9w | ||||||
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Title | Cryptococcus neoformans Hsp90 nucleotide binding domain in complex with BUCMD00461 | ||||||
Components | Hsp90-like protein | ||||||
Keywords | CHAPERONE / Cryptococcus / HSP90 / ATP-binding / Inhibitor | ||||||
Function / homology | Function and homology information ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Cryptococcus neoformans (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Kuntz, D.A. / Prive, G.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Fungal-Selective Resorcylate Aminopyrazole Hsp90 Inhibitors: Optimization of Whole-Cell Anticryptococcal Activity and Insights into the Structural Origins of Cryptococcal Selectivity. Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / ...Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / Whitesell, L. / Cowen, L.E. / Brown, L.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k9w.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k9w.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 7k9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/7k9w ftp://data.pdbj.org/pub/pdb/validation_reports/k9/7k9w | HTTPS FTP |
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-Related structure data
Related structure data | 7k9rC 7k9sC 7k9uC 7k9vC 6cjiS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24473.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans (fungus) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: J9VVA4 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1 M LiCl, 0.1 M Hepes or Cacodylate, 6.5 to 7, 20-25% PEG 6K, 10-20% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97932 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→29.48 Å / Num. obs: 27266 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0319 / Rrim(I) all: 0.045 / Net I/σ(I): 9.47 |
Reflection shell | Resolution: 2.13→2.19 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1770 / CC1/2: 0.791 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CJI Resolution: 2.13→29.48 Å / SU ML: 0.2488 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8478 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→29.48 Å
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Refine LS restraints |
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LS refinement shell |
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