7P19
Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2
- PDB DOI: https://doi.org/10.2210/pdb7P19/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes
- Deposited: 2021-07-01 Released: 2022-07-13
- Funding Organization(s): Other government
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.24 Å
- R-Value Free: 0.288
- R-Value Work: 0.231
- R-Value Observed: 0.234
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 |
| Processed angiotensin-converting enzyme 2 | A, C [auth B] | 599 | Homo sapiens | Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1 | |||||
PHAROS: Q9BYF1 GTEx: ENSG00000130234 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9BYF1 | ||||
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 protein S1 | B [auth E], D [auth C] | 210 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 1 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 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | E [auth A] G [auth A] I [auth E] K [auth B] M [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| ZN Query on ZN | F [auth A], L [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | H [auth A], N [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | J [auth E] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.24 Å
- R-Value Free: 0.288
- R-Value Work: 0.231
- R-Value Observed: 0.234
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 60.591 | α = 90 |
| b = 165.037 | β = 90 |
| c = 228.678 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| autoPROC | data reduction |
| autoPROC | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-07-13 Deposition Author(s): Erausquin, E., Lopez-Sagaseta, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other government | Spain | 0011-3597-2020-000010 |
| Other government | Spain | 0011-1408-2021-000023 |
Revision History (Full details and data files)
- Version 1.0: 2022-07-13
Type: Initial release - Version 1.1: 2022-12-21
Changes: Author supporting evidence, Database references - Version 1.2: 2024-01-31
Changes: Data collection, Refinement description
