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- PDB-6zlr: Soaking competent crystal form of the SARS-CoV-2 Receptor Binding... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zlr | ||||||
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Title | Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex. | ||||||
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![]() | VIRAL PROTEIN / SARS-COV-2 / VIRAL PROTEIN COMPLEX / ANTIBODY | ||||||
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / 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 | ![]() ![]() ![]() | ||||||
![]() | de Nicola, G.F. / Nichols, C.E. | ||||||
![]() | ![]() Title: A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface. Authors: Nichols, C. / Ng, J. / Keshu, A. / Fraternali, F. / De Nicola, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 383 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 503.5 KB | Display | ![]() |
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Full document | ![]() | 518.5 KB | Display | |
Data in XML | ![]() | 62.8 KB | Display | |
Data in CIF | ![]() | 85.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w41S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
#1: Protein | Mass: 26095.348 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() #2: Antibody | Mass: 23455.420 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 24376.963 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Sugar | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.13 Å3/Da / Density % sol: 76.02 % / Description: Thin Rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 0.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000 |
-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 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→68.028 Å / Num. obs: 72060 / % possible obs: 91.1 % / Redundancy: 4.7 % / CC1/2: 0.933 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 3.09→3.16 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4356 / CC1/2: 0.415 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6W41 Resolution: 3.1→68.028 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.885 / SU B: 19.006 / SU ML: 0.303 / Cross valid method: FREE R-VALUE / ESU R: 0.908 / ESU R Free: 0.375 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.64 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→68.028 Å
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Refine LS restraints |
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