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Yorodumi- PDB-7ba0: Structure of the FKBP51FK1 domain in complex with the macrocyclic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ba0 | ||||||
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Title | Structure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 63 | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE / Inhibitor / Complex / SAFit / FKBP | ||||||
Function / homology | Function and homology information FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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: 1.14 Å | ||||||
Authors | Bauder, M. / Meyners, C. / Purder, P. / Merz, S. / Voll, A. / Heymann, T. / Hausch, F. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Based Design of High-Affinity Macrocyclic FKBP51 Inhibitors. Authors: Bauder, M. / Meyners, C. / Purder, P.L. / Merz, S. / Sugiarto, W.O. / Voll, A.M. / Heymann, T. / Hausch, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ba0.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ba0.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ba0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ba0_validation.pdf.gz | 768.3 KB | Display | wwPDB validaton report |
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Full document | 7ba0_full_validation.pdf.gz | 769.1 KB | Display | |
Data in XML | 7ba0_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 7ba0_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/7ba0 ftp://data.pdbj.org/pub/pdb/validation_reports/ba/7ba0 | HTTPS FTP |
-Related structure data
Related structure data | 7a6wC 7a6xC 7awxC 7b9yC 7b9zC 4tw7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14273.369 Da / Num. of mol.: 1 / Mutation: A19T C103A C107I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-T5H / |
#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: 1.76 Å3/Da / Density % sol: 30.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 24% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.14→61.37 Å / Num. obs: 34112 / % possible obs: 90.9 % / Redundancy: 12.5 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Net I/σ(I): 12.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TW7 Resolution: 1.14→37.003 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.982 / WRfactor Rfree: 0.154 / WRfactor Rwork: 0.134 / SU B: 1.566 / SU ML: 0.031 / Average fsc free: 0.9324 / Average fsc work: 0.937 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.037 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.859 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→37.003 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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