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- PDB-8kgz: Crystal structure of single-chain Fv antibody against antigen pep... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8kgz | ||||||
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Title | Crystal structure of single-chain Fv antibody against antigen peptide from SARS-CoV2 S-spike protein | ||||||
![]() | Thioredoxin 1,scFv | ||||||
![]() | IMMUNE SYSTEM / ScFv / antibody / S-spike protein / antigen | ||||||
Function / homology | ![]() DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, Q.Q. / Zhang, B.L. / Cheng, X.Y. / Huang, Y.Q. / Su, Z.D. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of sheep scFv antibody against an antigen peptide of SARS-CoV2 S-spike protein Authors: Ma, Q.Q. / Zheng, B.L. / Cheng, X.Y. / Huang, Y.Q. / Su, Z.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 43198.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Gene: trxA, fipA, tsnC, b3781, JW5856 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.54 Å3/Da / Density % sol: 20.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M HEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→77.75 Å / Num. obs: 179188 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.882 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 6.4 % / Num. unique obs: 26361 / CC1/2: 0.882 |
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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: 26.916 Å2
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Refinement step | Cycle: 1 / Resolution: 2.21→55.79 Å
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Refine LS restraints |
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