[English] 日本語
![](img/lk-miru.gif)
- PDB-7k9w: Cryptococcus neoformans Hsp90 nucleotide binding domain in comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7k9w | ||||||
---|---|---|---|---|---|---|---|
Title | Cryptococcus neoformans Hsp90 nucleotide binding domain in complex with BUCMD00461 | ||||||
![]() | Hsp90-like protein | ||||||
![]() | CHAPERONE / Cryptococcus / HSP90 / ATP-binding / Inhibitor | ||||||
Function / homology | ![]() ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuntz, D.A. / Prive, G.G. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 107.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7k9rC ![]() 7k9sC ![]() 7k9uC ![]() 7k9vC ![]() 6cjiS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24473.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: J9VVA4 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|