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Open data
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Basic information
Entry | Database: PDB / ID: 8tud | ||||||
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Title | IgG1 Fc Heterodimer combYSelect2 | ||||||
![]() | (Immunoglobulin gamma-1 heavy chain) x 2 | ||||||
![]() | IMMUNE SYSTEM / IgG1 Fc / heterodimer | ||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Azzam, T. / Du, J.J. / Sundberg, E.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Combinatorially restricted computational design of protein-protein interfaces to produce IgG heterodimers. Authors: Azzam, T. / Du, J.J. / Flowers, M.W. / Ali, A.V. / Hunn, J.C. / Vijayvargiya, N. / Knagaram, R. / Bogacz, M. / Maravillas, K.E. / Sastre, D.E. / Fields, J.K. / Mirzaei, A. / Pierce, B.G. / Sundberg, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ttmC 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
#1: Antibody | Mass: 26132.570 Da / Num. of mol.: 1 / Mutation: D399Y, K447S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() | ||||
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#2: Antibody | Mass: 26146.555 Da / Num. of mol.: 1 / Mutation: K409S, T411Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() | ||||
#3: Polysaccharide | Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.67 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis Tris pH 6.5 and 29% PEG MME 2000 |
-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: Dec 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→42.36 Å / Num. obs: 11350 / % possible obs: 96.87 % / Redundancy: 11.5 % / Biso Wilson estimate: 50.24 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.453 / Rpim(I) all: 0.137 / Rrim(I) all: 0.474 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 3→3.108 Å / Redundancy: 10.7 % / Rmerge(I) obs: 3.074 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 993 / CC1/2: 0.628 / Rpim(I) all: 0.949 / Rrim(I) all: 3.221 / % possible all: 86.27 |
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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: 54.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→42.36 Å
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Refine LS restraints |
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LS refinement shell |
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