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Yorodumi- PDB-6tx7: CRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tx7 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPLEX WITH 2-PIPERIDONE | ||||||
Components | Peptidyl-prolyl cis-trans isomerase FKBP5 | ||||||
Keywords | ISOMERASE / PPIase / Fragment | ||||||
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 / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | ||||||
Authors | Fiegen, D. / Draxler, S.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Hybrid Screening Approach for Very Small Fragments: X-ray and Computational Screening on FKBP51. Authors: Draxler, S.W. / Bauer, M. / Eickmeier, C. / Nadal, S. / Nar, H. / Rangel Rojas, D. / Seeliger, D. / Zeeb, M. / Fiegen, D. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tx7.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tx7.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 6tx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/6tx7 ftp://data.pdbj.org/pub/pdb/validation_reports/tx/6tx7 | HTTPS FTP |
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-Related structure data
Related structure data | 6tx4C 6tx5C 6tx6C 6tx8C 6tx9C 6txxC 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 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-CL / | ||||||
#3: Chemical | #4: Chemical | #5: 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: 47.32 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28-41% PEG3350, 0.2 M NH4OAc, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→56.69 Å / Num. obs: 49285 / % possible obs: 98.6 % / Redundancy: 6 % / Biso Wilson estimate: 13.04 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.014 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.13→1.133 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 432 / CC1/2: 0.8 / Rpim(I) all: 0.323 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3o5q Resolution: 1.13→39.28 Å / SU ML: 0.0803 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.3914 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→39.28 Å
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Refine LS restraints |
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LS refinement shell |
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