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- PDB-6iqh: X-ray crystal structure of covalent-bonded complex of Fc and peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iqh | ||||||||||||
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Title | X-ray crystal structure of covalent-bonded complex of Fc and peptide | ||||||||||||
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![]() | IMMUNE SYSTEM / Fc / Complex | ||||||||||||
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 | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Adachi, M. / Ito, Y. | ||||||||||||
![]() | ![]() Title: Site-Specific Chemical Conjugation of Antibodies by Using Affinity Peptide for the Development of Therapeutic Antibody Format. Authors: Kishimoto, S. / Nakashimada, Y. / Yokota, R. / Hatanaka, T. / Adachi, M. / Ito, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iqgC ![]() 1dn2S S: Starting model for refinement 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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Components
#1: Antibody | Mass: 23788.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2063.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Polysaccharide | 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: 3.18 Å3/Da / Density % sol: 61.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 0.1 M CHES pH 10.0, 0.3M NaCl, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.999→44.1 Å / Num. obs: 12253 / % possible obs: 98.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1158 / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DN2 Resolution: 2.999→44.1 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.999→44.1 Å
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Refine LS restraints |
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LS refinement shell |
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