[English] 日本語
![](img/lk-miru.gif)
- PDB-5njx: Human FKBP51 protein in complex with C-terminal peptide of Human ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5njx | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human FKBP51 protein in complex with C-terminal peptide of Human HSP 90-alpha | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | ISOMERASE / HSP90 / FKBP51 / TPR / C-terminal peptide of HSP90 | |||||||||||||||||||||
Function / homology | ![]() FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ATP-dependent protein folding chaperone / response to bacterium ...FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ATP-dependent protein folding chaperone / response to bacterium / disordered domain specific binding / unfolded protein binding / protein folding / myelin sheath / protein-macromolecule adaptor activity / cellular response to heat / protein stabilization / neuronal cell body / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Kumar, R. / Moche, M. / Winblad, B. / Pavlov, P. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51. Authors: Kumar, R. / Moche, M. / Winblad, B. / Pavlov, P.F. | |||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 186 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450.1 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ompC ![]() 1kt0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 51701.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The full length human FKBP51 containing first 5 N-terminus amino acids from the expression vector. Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Protein/peptide | Mass: 2026.089 Da / Num. of mol.: 1 / Fragment: UNP residues 413-422 / Source method: obtained synthetically Details: The peptide contains 10 amino acids from C- terminal of human HSP 90-alpha Source: (synth.) ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.17 % Preparation: The completeness of our data is low to 2.49A resolution being 62% overall and 2.5% in the highest resolution shell since we kept only the strongest reflections in each direction. This is ...Preparation: The completeness of our data is low to 2.49A resolution being 62% overall and 2.5% in the highest resolution shell since we kept only the strongest reflections in each direction. This is the purpose of the diffraction anisotropy server (https://services.mbi.ucla.edu/anisoscale/) and also staraniso (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). We used the diffraction anisotropy server to keep the good reflections only for structure refinement |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 18 %w/v PEG MME 5K, 0.2 M NH4SO4, 0.1 M MES pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→44 Å / Num. obs: 280852 / % possible obs: 62.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.36 % / Biso Wilson estimate: 57.38 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.49→2.55 Å / Redundancy: 17 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 3.84 / Num. measured obs: 733 / Num. unique all: 43 / Num. unique obs: 43 / CC1/2: 0.959 / Rsym value: 0.756 / % possible all: 2.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1KT0 Resolution: 2.49→44 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.838 / SU R Cruickshank DPI: 1.839 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377 / SU Rfree Cruickshank DPI: 0.373
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.32 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.49→44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.49→2.69 Å / Total num. of bins used: 7
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -34.3543 Å / Origin y: 38.7724 Å / Origin z: -10.9071 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: { A|* } |