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Open data
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Basic information
Entry | Database: PDB / ID: 8coh | ||||||
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Title | Structure of the complement C5 specific nanobody TPP-3444 | ||||||
![]() | Nanobody TPP-3444 | ||||||
![]() | IMMUNE SYSTEM / innate immunity / complement / terminal pathway / nanobody / antigen-antibody complex | ||||||
Function / homology | CITRIC ACID / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pedersen, D.V. / Andersen, G.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of the bispecific VHH antibody gefurulimab (ALXN1720) targeting complement component 5, and designed for low volume subcutaneous administration. Authors: Jindal, S. / Pedersen, D.V. / Gera, N. / Chandler, J. / Patel, R. / Neill, A. / Cone, J. / Zhang, Y. / Yuan, C.X. / Millman, E.E. / Carlin, D. / Puffer, B. / Sheridan, D. / Andersen, G.R. / Tamburini, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.5 KB | Display | ![]() |
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Full document | ![]() | 787.6 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8coeC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 14627.962 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-MN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.1 Details: 54 mM citric acid, 36 mM BIS-TRIS propane pH 4.1, 14.4% w/v polyethylene glycol 3350, and 10 mM NiCl2. |
-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: Nov 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→36.44 Å / Num. obs: 30885 / % possible obs: 99.94 % / Redundancy: 25.9 % / Biso Wilson estimate: 12.47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1071 / Net I/σ(I): 22.55 |
Reflection shell | Resolution: 1.3→1.347 Å / Redundancy: 25 % / Rmerge(I) obs: 1.447 / Num. unique obs: 3019 / CC1/2: 0.884 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→36.44 Å
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Refine LS restraints |
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LS refinement shell |
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