7BZ5
Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody
- PDB DOI: https://doi.org/10.2210/pdb7BZ5/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Spodoptera frugiperda, Homo sapiens
- Mutation(s): No 
- Deposited: 2020-04-26 Released: 2020-05-13 
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.191 
- R-Value Work: 0.167 
- R-Value Observed: 0.168 
This is version 1.5 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike protein S1 | 229 | 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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Heavy chain of B38 | B [auth H] | 222 | Homo sapiens | 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: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Light chain of B38 | C [auth L] | 218 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 | D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.191 
- R-Value Work: 0.167 
- R-Value Observed: 0.168 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 195.226 | α = 90 |
b = 86.417 | β = 100.19 |
c = 56.827 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
Funding Organization | Location | Grant Number |
---|---|---|
National Natural Science Foundation of China (NSFC) | China | 31872745, 81902058 |
Revision History (Full details and data files)
- Version 1.0: 2020-05-13
Type: Initial release - Version 1.1: 2020-05-27
Changes: Database references - Version 1.2: 2020-06-24
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2021-03-10
Changes: Structure summary - Version 1.5: 2023-11-29
Changes: Data collection, Database references, Refinement description