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- PDB-8chm: Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8chm | ||||||
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Title | Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase FKBP1A | ||||||
![]() | ISOMERASE / FKBP12 / Inhibitor | ||||||
Function / homology | ![]() macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / 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 ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / 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 / FK506 binding / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / 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 / regulation of protein localization / SARS-CoV-1 activates/modulates innate immune responses / 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 / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meyners, C. / Purder, P.L. / Hausch, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogues. Authors: Purder, P.L. / Meyners, C. / Sugiarto, W.O. / Kolos, J. / Lohr, F. / Gebel, J. / Nehls, T. / Dotsch, V. / Lermyte, F. / Hausch, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.6 KB | Display | ![]() |
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PDB format | ![]() | 81.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8chiC ![]() 8chjC ![]() 8chkC ![]() 8chlC ![]() 8chnC ![]() 8chpC ![]() 8chqC ![]() 8chrC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11832.496 Da / Num. of mol.: 1 / Mutation: C22V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 225 molecules ![](data/chem/img/UT6.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-UT6 / ( | ||||||
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#3: Chemical | ChemComp-DMS / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.1 M ammonium sulfate, 0.2 M cadmium chloride, 0.1M HEPES-NaOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 10, 2022 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.12→45.648 Å / Num. obs: 50936 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.015 / Rrim(I) all: 0.03 / Net I/σ(I): 30.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() 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: 10.321 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→45.648 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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