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Open data
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Basic information
Entry | Database: PDB / ID: 1bl4 | ||||||
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Title | FKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND | ||||||
![]() | PROTEIN (FK506 BINDING PROTEIN) | ||||||
![]() | ISOMERASE / ROTAMASE | ||||||
Function / homology | ![]() extrinsic component of organelle membrane / : / 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 ...extrinsic component of organelle membrane / : / 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 / ventricular cardiac muscle tissue morphogenesis / 'de novo' protein folding / 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 / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / 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) / peptidylprolyl isomerase / sarcoplasmic reticulum / 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 / amyloid fibril formation / Potential therapeutics for SARS / intracellular membrane-bounded organelle / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hatada, M.H. / Clackson, T. / Yang, W. / Rozamus, L.W. / Amara, J. / Rollins, C.T. / Stevenson, L.F. / Magari, S.R. / Wood, S.A. / Courage, N.L. ...Hatada, M.H. / Clackson, T. / Yang, W. / Rozamus, L.W. / Amara, J. / Rollins, C.T. / Stevenson, L.F. / Magari, S.R. / Wood, S.A. / Courage, N.L. / Lu, X. / Cerasoli Junior, F. / Gilman, M. / Holt, D. | ||||||
![]() | ![]() Title: Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity. Authors: Clackson, T. / Yang, W. / Rozamus, L.W. / Hatada, M. / Amara, J.F. / Rollins, C.T. / Stevenson, L.F. / Magari, S.R. / Wood, S.A. / Courage, N.L. / Lu, X. / Cerasoli Jr., F. / Gilman, M. / Holt, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 505.1 KB | Display | ![]() |
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Full document | ![]() | 511.7 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fkfS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11788.465 Da / Num. of mol.: 2 / Mutation: F36V Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH REDESIGNED COMPOUND / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P62942, UniProt: P20071, peptidylprolyl isomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: VAPOR DIFFUSION IN HANGING DROPS WITH 40 MG/ML COMPLEX AND 1.2M AMMONIUM SULFATE, 0.1M SODIUM PHOSPHATE, PH 6.0 OVER RESERVOIRS OF 2.4 M AMMONIUM SULFATE, vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 15, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 16490 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.16 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FKF Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.25 / % reflection Rfree: 10 % / Rfactor Rwork: 0.237 |