+Open data
-Basic information
Entry | Database: PDB / ID: 8r5k | ||||||
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Title | The Fk1 domain of FKBP51 in complex with Antascomicine B | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 Å | ||||||
Authors | Voll, M.A. / Bracher, A. / Hausch, F. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2024 Title: Antascomicin B stabilizes FKBP51-Akt1 complexes as a molecular glue. Authors: Schafer, S.C. / Voll, A.M. / Bracher, A. / Ley, S.V. / Hausch, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r5k.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r5k.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 8r5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/8r5k ftp://data.pdbj.org/pub/pdb/validation_reports/r5/8r5k | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14026.077 Da / Num. of mol.: 1 / Mutation: A19T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Plasmid: pProEx-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-Y6Z / Mass: 675.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H57NO10 / Feature type: SUBJECT OF INVESTIGATION |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 32 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5 Macroseeding after 21 d, big crystalls after further 3 d |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.85 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→39.4 Å / Num. obs: 101663 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.983 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 0.89→0.9 Å / Num. unique obs: 4946 / CC1/2: 0.678 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.89→28.74 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.977 / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 13.246 Å2
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Refinement step | Cycle: LAST / Resolution: 0.89→28.74 Å
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LS refinement shell | Resolution: 0.901→0.924 Å /
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