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Yorodumi- PDB-7aou: The Fk1 domain of FKBP51 in complex with (2'R,5'S,12'R)-12'-cyclo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aou | ||||||
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Title | The Fk1 domain of FKBP51 in complex with (2'R,5'S,12'R)-12'-cyclohexyl-2'-[2-(3,4-dimethoxyphenyl)ethyl]-3',19'-dioxa-10',13',16'-triazaspiro[cyclopropane-1,15'- tricyclo[18.3.1.0-5,10]tetracosane]-1'(24'),20',22'-triene-4',11',14',17'-tetrone | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE / FKBP51 / chaperone / immunophilin / macrocycle / transient binding pocket | ||||||
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 / molecular replacement / Resolution: 1.16 Å | ||||||
Authors | Voll, M.A. / Meyners, C. / Heymann, T. / Merz, S. / Purder, P. / Bracher, A. / Hausch, F. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Macrocyclic FKBP51 Ligands Define a Transient Binding Mode with Enhanced Selectivity. Authors: Voll, A.M. / Meyners, C. / Taubert, M.C. / Bajaj, T. / Heymann, T. / Merz, S. / Charalampidou, A. / Kolos, J. / Purder, P.L. / Geiger, T.M. / Wessig, P. / Gassen, N.C. / Bracher, A. / Hausch, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aou.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aou.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 7aou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/7aou ftp://data.pdbj.org/pub/pdb/validation_reports/ao/7aou | HTTPS FTP |
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-Related structure data
Related structure data | 7aotC 7awfC 3o5qS 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: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13451, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-RTT / ( |
#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: 2.28 Å3/Da / Density % sol: 46.06 % |
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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 HEPES-NaOH pH 7.5 |
-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: 0.972422 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: 0.972422 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.16→38.06 Å / Num. obs: 44967 / % possible obs: 99.8 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.035 / Rrim(I) all: 0.05 / Net I/σ(I): 9.8 / Num. measured all: 85193 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.576
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O5Q Resolution: 1.16→29.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.276 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036 / 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: 70.46 Å2 / Biso mean: 17.696 Å2 / Biso min: 8.44 Å2
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Refinement step | Cycle: final / Resolution: 1.16→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.161→1.191 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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