Research workbench
Cryo-EM structure of SARS-cov-2 omicron spike receptor-binding domain in complex with mouse ACE2
Analyse Cryo-EM structure of SARS-cov-2 omicron spike receptor-binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WRI
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike glycoprotein
- UniProt
- Q8R0I0, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 5 · best druggability 0.73
Structure
electron microscopy · 2 distinct chains · 41% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 595 | 53% helix, 3% strand | Q8R0I0 |
| B | Spike glycoprotein | protein | 195 | 7% helix, 27% strand | P0DTC2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.73 | 0.79 | 65 | empty |
| 2 | 413 | 0.69 | 0.81 | 41 | empty |
| 3 | 110 | 0.64 | 0.88 | 22 | empty |
| 4 | 52 | 0.27 | 0.74 | 14 | empty |
| 5 | 52 | 0.25 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 741 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WRI · Cryo-EM structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8R0I0 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q8R0I0) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8R0I0
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7WRI · PDBe 7WRI · UniProt Q8R0I0 · UniProt P0DTC2
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