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Open data
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Basic information
Entry | Database: PDB / ID: 5dk2 | |||||||||
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Title | Fc Heterodimer E356K/D399K + K392D/K409D | |||||||||
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![]() | IMMUNE SYSTEM / Heterodimer / Immunoglobulin / CH3 / Fc / Bispecific Antibody | |||||||||
Function / homology | ![]() Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
Model details | Design XXX | |||||||||
![]() | Atwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. ...Atwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. / Fitchett, J.R. / Gutierrez, B. / Hendle, J. / Demarest, S.J. / Kuhlman, B. | |||||||||
![]() | ![]() Title: Computationally Designed Bispecific Antibodies using Negative State Repertoires. Authors: Leaver-Fay, A. / Froning, K.J. / Atwell, S. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Hassanali, S. / Chamberlain, A.K. / Fitchett, J.R. / Demarest, S.J. / Kuhlman, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.4 KB | Display | ![]() |
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PDB format | ![]() | 112.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5di8C ![]() 5dj0C ![]() 5dj2C ![]() 5dj6C ![]() 5dj8C ![]() 5djaC ![]() 5djcC ![]() 5djdC ![]() 5djxC ![]() 5djyC ![]() 5djzC ![]() 5dk0C ![]() 5dvkC ![]() 5dvlC ![]() 5dvmC ![]() 5dvnC ![]() 5dvoC 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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2 | ![]()
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Unit cell |
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Components
-Ig gamma-1 chain C ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 25627.176 Da / Num. of mol.: 2 / Fragment: UNP residues 104-330 / Mutation: E356K, D399K Source method: isolated from a genetically manipulated source Details: transient expression / Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 26954.121 Da / Num. of mol.: 2 / Fragment: UNP residues 104-330 / Mutation: K392D, K409D Source method: isolated from a genetically manipulated source Details: transient expression / Source: (gene. exp.) ![]() ![]() |
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-Protein/peptide / Non-polymers , 2 types, 106 molecules C![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1533.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CPC Scientific Inc., Sunnyvale CA / Source: (synth.) synthetic construct (others) |
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#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 3 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: 100mM MES pH 6.5 + 12% PEG 8K + 200mM Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 193 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 13, 2014 / Details: Diamond (111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→30 Å / Num. obs: 37058 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.103 / Rsym value: 0.073 / Net I/av σ(I): 9.744 / Net I/σ(I): 11.1 / Num. measured all: 126900 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.122 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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