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- PDB-7ytq: Human langerin carbohydrate recognition domain in complex with an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ytq | ||||||
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Title | Human langerin carbohydrate recognition domain in complex with an alpha-mannoside ligand | ||||||
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![]() | SUGAR BINDING PROTEIN / Langerin / lectin / innate immunity / C-type | ||||||
Function / homology | ![]() carbohydrate binding / defense response to virus / membrane => GO:0016020 / external side of plasma membrane Similarity search - Function | ||||||
Biological species | ![]() unidentified (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wangkanont, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human langerin carbohydrate recognition domain in complex with an alpha-mannoside ligand Authors: Wangkanont, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.4 KB | Display | ![]() |
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PDB format | ![]() | 109.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3c22S S: Starting model for refinement |
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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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 17949.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 291.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 674 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/JMI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/JMI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-JMI / ~{ #5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-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 Å3/Da / Density % sol: 38.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES, 200 mM MgCl2, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 23, 2022 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.6→19.94 Å / Num. obs: 74724 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.033 / Rrim(I) all: 0.092 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3C22 Resolution: 1.6→19.94 Å / SU ML: 0.1848 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6538 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: 24.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.94 Å
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Refine LS restraints |
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LS refinement shell |
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