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- PDB-8bsf: CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bsf | ||||||
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Title | CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab | ||||||
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![]() | VIRAL PROTEIN / ANTIBODY / VIRUS / COMPLEX / SARS-COV-2 / VIRAL PROTEIN COMPLEX | ||||||
Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Welin, M. / Kimbung, Y.R. / Focht, D. / Pisitkun, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants. Authors: Boonkrai, C. / Cotrone, T.S. / Chaisuriyong, W. / Tantawichien, T. / Thisyakorn, U. / Fernandez, S. / Hunsawong, T. / Reed, M. / Wongtangprasert, T. / Audomsun, T. / Phakham, T. / ...Authors: Boonkrai, C. / Cotrone, T.S. / Chaisuriyong, W. / Tantawichien, T. / Thisyakorn, U. / Fernandez, S. / Hunsawong, T. / Reed, M. / Wongtangprasert, T. / Audomsun, T. / Phakham, T. / Attakitbancha, C. / Saelao, P. / Focht, D. / Kimbung, R. / Welin, M. / Malik, A.A. / Pisitkun, T. / Srisawat, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138 KB | Display | ![]() |
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PDB format | ![]() | 103.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.5 KB | Display | ![]() |
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Full document | ![]() | 480.5 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bseC 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
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24568.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 22861.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 26129.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Beta variant with the following mutations, K417N, E484K, N501Y Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 127 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.04 M potassium dihydrogen phosphate 18 % PEG 8000 20 % glycerol |
-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: Oct 28, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.07 Å / Num. obs: 44882 / % possible obs: 98.9 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Χ2: 1.01 / Net I/σ(I): 13 / Num. measured all: 317904 |
Reflection shell | Resolution: 2.2→2.27 Å / % possible obs: 98.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.568 / Num. measured all: 27580 / Num. unique obs: 3839 / CC1/2: 0.575 / Rpim(I) all: 0.627 / Rrim(I) all: 1.69 / Χ2: 0.92 / Net I/σ(I) obs: 1.3 |
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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: 53.945 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→48.07 Å
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