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- PDB-8acf: Structure of the argX-117 in complex with a complement C2 fragmen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8acf | ||||||
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Title | Structure of the argX-117 in complex with a complement C2 fragment at low pH | ||||||
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![]() | IMMUNE SYSTEM / Innate immune system / complement / antibody | ||||||
Function / homology | ![]() classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / response to nutrient / complement activation, classical pathway / Regulation of Complement cascade ...classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / response to nutrient / complement activation, classical pathway / Regulation of Complement cascade / response to bacterium / response to lipopolysaccharide / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Olesen, H.G. / Andersen, G.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-function analysis of ARGX-117, a calcium- and pH-dependent clinical phase complement C2 blocking antibody Authors: Olesen, H.G. / Andersen, G.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 484 KB | Display | ![]() |
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PDB format | ![]() | 329.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 839.6 KB | Display | ![]() |
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Full document | ![]() | 843.2 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aciC ![]() 6aniS S: Starting model for refinement 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
-Antibody , 3 types, 3 molecules HKL
#2: Antibody | Mass: 23450.080 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 14204.509 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Antibody | Mass: 23957.604 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 20991.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 333 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 50% MPD, 100 mM Hepes pH 5.5-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.57 Å / Num. obs: 87785 / % possible obs: 99.97 % / Redundancy: 13.4 % / Biso Wilson estimate: 38.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.457 / Num. unique obs: 8651 / CC1/2: 0.472 / % possible all: 99.98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ANI Resolution: 1.8→44.57 Å / SU ML: 0.2567 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5515 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: 48.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→44.57 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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