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 | |||||
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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
