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Open data
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Basic information
Entry | Database: PDB / ID: 2j0y | |||||||||
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Title | L-ficolin complexed to b-1,3-D-glucan | |||||||||
![]() | FICOLIN-2 | |||||||||
![]() | LECTIN / GLYCOPROTEIN / FICRINOGEN-LIKE / INNATE IMMUNITY / PATTERN RECOGNITION PROTEIN / COLLAGEN / IMMUNOLOGY / LECTIN- LIKE | |||||||||
Function / homology | ![]() mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer ...mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer / serine-type endopeptidase complex / proteoglycan binding / Initial triggering of complement / antigen binding / calcium-dependent protein binding / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / blood microparticle / defense response to Gram-positive bacterium / external side of plasma membrane / signaling receptor binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Garlatti, V. / Gaboriaud, C. | |||||||||
![]() | ![]() Title: Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins. Authors: Garlatti, V. / Belloy, N. / Martin, L. / Lacroix, M. / Matsushita, M. / Endo, Y. / Fujita, T. / Fontecilla-Camps, J.C. / Arlaud, G.J. / Thielens, N.M. / Gaboriaud, C. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.2 KB | Display | ![]() |
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PDB format | ![]() | 216.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 51.1 KB | Display | |
Data in CIF | ![]() | 70.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j0gC ![]() 2j0hC ![]() 2j1gC ![]() 2j2pC ![]() 2j3fC ![]() 2j3gC ![]() 2j3oC ![]() 2j3uC ![]() 2j5zC ![]() 2j60C ![]() 2j61C ![]() 2j64C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 24729.318 Da / Num. of mol.: 6 / Fragment: C-TERMINAL BINDING DOMAIN, RESIDUES 96-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 7 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | #7: Sugar | ChemComp-BGC / | |
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-Non-polymers , 3 types, 301 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ACT / | ||
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#5: Chemical | ChemComp-CA / #8: Water | ChemComp-HOH / | |
-Details
Compound details | CALCIUM-DEPENDENT AND GLCNAC-BINDING LECTIN. |
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Sequence details | C-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATES: THERE IS A DIFFERENCE BECAUSE ...C-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 50.8 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0718 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→19.95 Å / Num. obs: 58888 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.35→19.95 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.678 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE A AND D CHAIN ARE NOT CLEARLY DEFINE IN DENSITY BECAUSE THEY ARE QUITE FLEXIBLE.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→19.95 Å
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Refine LS restraints |
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