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Open data
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Basic information
Entry | Database: PDB / ID: 6ydb | ||||||
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Title | Human wtSTING in complex with 2',2'-difluoro-3',3'-c-di-GMP | ||||||
![]() | Stimulator of interferon protein | ||||||
![]() | PROTEIN BINDING / innate immune system / cyclic dinucleotide / STING | ||||||
Function / homology | ![]() 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Boura, E. / Smola, M. | ||||||
![]() | ![]() Title: Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein. Authors: Smola, M. / Gutten, O. / Dejmek, M. / Kozisek, M. / Evangelidis, T. / Tehrani, Z.A. / Novotna, B. / Nencka, R. / Birkus, G. / Rulisek, L. / Boura, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.1 KB | Display | ![]() |
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PDB format | ![]() | 59 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 794.7 KB | Display | ![]() |
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Full document | ![]() | 795.5 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y99C ![]() 6ydzC ![]() 6yeaC ![]() 6z0zC ![]() 6z15C ![]() 4ksyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23189.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GGF / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium chloride, 0.1 M Na/K phosphate pH 6.2, 40% (v/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.801→39.275 Å / Num. obs: 5861 / % possible obs: 99.07 % / Redundancy: 15.7 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 9.71 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 561 / CC1/2: 0.581 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KSY Resolution: 2.801→39.2741 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 129.11 Å2 / Biso mean: 65.9723 Å2 / Biso min: 36.86 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.801→39.2741 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %
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