+Open data
-Basic information
Entry | Database: PDB / ID: 6ysc | ||||||
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Title | GLYCOSYLATED KNOB-HOLE/DUMMY FC FRAGMENT | ||||||
Components | (Immunoglobulin gamma-1 heavy chain) x 2 | ||||||
Keywords | IMMUNE SYSTEM / BISPECIFIC ANTIBODY / FC ENGINEERING / KNOB-INTO-HOLE / FORCE / FORMAT CHAIN EXCHANGE | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kuglstatter, A. / Leibrock, L. / Benz, J. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Format chain exchange (FORCE) for high-throughput generation of bispecific antibodies in combinatorial binder-format matrices. Authors: Dengl, S. / Mayer, K. / Bormann, F. / Duerr, H. / Hoffmann, E. / Nussbaum, B. / Tischler, M. / Wagner, M. / Kuglstatter, A. / Leibrock, L. / Buldun, C. / Georges, G. / Brinkmann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ysc.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ysc.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ysc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ysc_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6ysc_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6ysc_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 6ysc_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/6ysc ftp://data.pdbj.org/pub/pdb/validation_reports/ys/6ysc | HTTPS FTP |
-Related structure data
Related structure data | 6yt7C 6ytbC 5hy9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25682.125 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: KNOB PROTEIN (S354C,T366W) / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 | ||||
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#2: Antibody | Mass: 26984.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HOLE-DUMMY PROTEIN (E357K,T366S,L368A,Y407V) / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 | ||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15% (w/v) PEG4000, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→71.01 Å / Num. obs: 24877 / % possible obs: 94.8 % / Redundancy: 6.5 % / CC1/2: 1 / Rpim(I) all: 0.024 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.05→2.21 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1310 / CC1/2: 0.64 / Rpim(I) all: 0.423 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HY9 Resolution: 2.05→71.01 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 126.68 Å2 / Biso mean: 47.8893 Å2 / Biso min: 18.28 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→71.01 Å
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