7JMP
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39
- PDB DOI: https://doi.org/10.2210/pdb7JMP/pdb
- Classification: Viral Protein/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Trichoplusia ni, Mus musculus
- Mutation(s): No 
- Deposited: 2020-08-02 Released: 2020-08-26 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.209 
- R-Value Work: 0.177 
- R-Value Observed: 0.178 
This is version 1.2 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 | 231 | 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 |
COVA2-39 heavy chain | B [auth H] | 232 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
COVA2-39 light chain | C [auth L] | 216 | 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: 1.71 Å
- R-Value Free: 0.209 
- R-Value Work: 0.177 
- R-Value Observed: 0.178 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 68.905 | α = 90 |
b = 80.445 | β = 104.88 |
c = 72.006 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-08-26  Deposition Author(s): Wu, N.C., Yuan, M., Liu, H., Zhu, X., Wilson, I.A.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI139445 |
Bill & Melinda Gates Foundation | OPP1170236 | |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | AI110657 |
Revision History (Full details and data files)
- Version 1.0: 2020-08-26
Type: Initial release - Version 1.1: 2022-02-23
Changes: Database references - Version 1.2: 2023-10-18
Changes: Data collection, Refinement description