7VOA
Crystal structure of SARS-CoV-2 RBD in complex with aRBD5
- PDB DOI: https://doi.org/10.2210/pdb7VOA/pdb
- Classification: VIRAL PROTEIN/ANTIVIRAL PROTEIN
- Organism(s): Vicugna pacos, Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli, Eukaryota sp.
- Mutation(s): No 
- Deposited: 2021-10-13 Released: 2022-08-10 
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.226 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
alpaca nanobody | 128 | Vicugna pacos | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike glycoprotein | 208 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0  Gene Names: S, 2 | ||
UniProt | |||||
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0DTC2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | C [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.226 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 53.44 | α = 90 |
b = 87.7 | β = 90 |
c = 89.05 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-08-10  Deposition Author(s): Ma, H., Zeng, W.H., Jin, T.C.
Funding Organization | Location | Grant Number |
---|---|---|
National Natural Science Foundation of China (NSFC) | China | 31870731 |
National Natural Science Foundation of China (NSFC) | China | U1732109 |
Revision History (Full details and data files)
- Version 1.0: 2022-08-10
Type: Initial release - Version 1.1: 2022-08-17
Changes: Database references - Version 1.2: 2022-09-14
Changes: Database references - Version 1.3: 2023-11-29
Changes: Data collection, Refinement description