6M0J
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
- PDB DOI: https://doi.org/10.2210/pdb6M0J/pdb
- Classification: VIRAL PROTEIN/HYDROLASE
- Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2020-02-21 Released: 2020-03-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.227 
- R-Value Work: 0.192 
- R-Value Observed: 0.194 
This is version 2.6 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 |
Angiotensin-converting enzyme 2 | 603 | Homo sapiens | Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data) | ||
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] | 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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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A], F [auth A], G [auth A], H [auth A], I [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CL Query on CL | D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.227 
- R-Value Work: 0.192 
- R-Value Observed: 0.194 
- Space Group: P 41 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 104.67 | α = 90 |
b = 104.67 | β = 90 |
c = 228.72 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
Revision History (Full details and data files)
- Version 1.0: 2020-03-18
Type: Initial release - Version 2.0: 2020-04-08
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary - Version 2.1: 2020-04-15
Changes: Database references - Version 2.2: 2020-05-06
Changes: Database references, Source and taxonomy, Structure summary - Version 2.3: 2020-05-27
Changes: Database references - Version 2.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.5: 2021-03-10
Changes: Structure summary - Version 2.6: 2023-11-29
Changes: Data collection, Database references, Refinement description