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Yorodumi- PDB-1fkj: ATOMIC STRUCTURE OF FKBP12-FK506, AN IMMUNOPHILIN IMMUNOSUPPRESSA... -
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-Basic information
Entry | Database: PDB / ID: 1fkj | ||||||
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Title | ATOMIC STRUCTURE OF FKBP12-FK506, AN IMMUNOPHILIN IMMUNOSUPPRESSANT COMPLEX | ||||||
Components | FK506 BINDING PROTEINFKBP | ||||||
Keywords | ROTAMASE / FK506 BINDING PROTEIN / FKBP12 / CIS-TRANS PROLYL-ISOMERASE | ||||||
Function / homology | Function and homology information macrolide binding / activin receptor binding / cytoplasmic side of membrane / signaling receptor inhibitor activity / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / signaling receptor inhibitor activity / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / Potential therapeutics for SARS / amyloid fibril formation / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Wilson, K.P. / Sintchak, M.D. / Thomson, J.A. / Navia, M.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin. Authors: Wilson, K.P. / Yamashita, M.M. / Sintchak, M.D. / Rotstein, S.H. / Murcko, M.A. / Boger, J. / Thomson, J.A. / Fitzgibbon, M.J. / Black, J.R. / Navia, M.A. #1: Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: X-Ray Structure of Calcineurin Inhibited by the Immunophilin-Immunosuppressant Fkbp12-Fk506 Complex Authors: Griffith, J.P. / Kim, J.L. / Kim, E.E. / Sintchak, M.D. / Thomson, J.A. / Fitzgibbon, M.J. / Fleming, M.A. / Caron, P.R. / Hsiao, K. / Navia, M.A. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Improved Calcineurin Inhibition by Yeast Fkbp12-Drug Complexes. Crystallographic and Functional Analysis Authors: Rotonda, J. / Burbaum, J.J. / Chan, H.K. / Marcy, A.I. / Becker, J.W. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Fk-506-Binding Protein: Three-Dimensional Structure of the Complex with the Antagonist L-685,818 Authors: Becker, J.W. / Rotonda, J. / Mckeever, B.M. / Chan, H.K. / Marcy, A.I. / Wiederrecht, G. / Hermes, J.D. / Springer, J.P. #4: Journal: J.Mol.Biol. / Year: 1993 Title: Atomic Structures of Human Immunophilin Fkbp-12 Complexes with Fk506 and Rapamycin Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J. #5: Journal: J.Am.Chem.Soc. / Year: 1991 Title: Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex Authors: Van Duyne, G.D. / Standaert, R.F. / Schreiber, S.L. / Clardy, J. #6: Journal: Science / Year: 1991 Title: Atomic Structure of Fkbp-Fk506, an Immunophilin-Immunosuppressant Complex Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fkj.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fkj.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/1fkj ftp://data.pdbj.org/pub/pdb/validation_reports/fk/1fkj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11836.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MR 12,000 DALTONS / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-FK5 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.02 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.54 |
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Detector | Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 1.7→7 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.7→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_improper_angle_deg / Dev ideal: 1.15 |