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- PDB-7ett: The FK1 domain of FKBP51 in complex with peptide-inhibitor hit QFPFV -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ett | ||||||
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Title | The FK1 domain of FKBP51 in complex with peptide-inhibitor hit QFPFV | ||||||
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![]() | ISOMERASE | ||||||
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 / response to bacterium / protein folding ...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 / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, J.T. / Zhu, Y.C. / Pan, D.B. / Xue, H.X. / Wang, S. / Liu, H.X. / He, Y.X. / Yao, X.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of pentapeptide-inhibitor hits targeting FKBP51 by combining computational modeling and X-ray crystallography. Authors: Han, J.T. / Zhu, Y. / Pan, D.B. / Xue, H.X. / Wang, S. / Peng, Y. / Liu, H. / He, Y.X. / Yao, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.3 KB | Display | ![]() |
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PDB format | ![]() | 26.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.5 KB | Display | ![]() |
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Full document | ![]() | 422.5 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7etuC ![]() 7etvC ![]() 3o5rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 636.737 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: peptide-inhibitor obtained via structure based drug design Source: (synth.) synthetic construct (others) |
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#2: Protein | Mass: 14026.077 Da / Num. of mol.: 1 / Mutation: A19T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.45 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 30%-36% PEG 3350, 0.2 M Ammonium Acetate and 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 21382 / % possible obs: 100 % / Redundancy: 11.6 % / Rpim(I) all: 0.035 / Net I/σ(I): 21.29 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1044 / Rpim(I) all: 0.06 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3O5R Resolution: 1.5→27.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.078 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.75 Å2 / Biso mean: 15.927 Å2 / Biso min: 8.14 Å2
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Refinement step | Cycle: final / Resolution: 1.5→27.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.541 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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