Research workbench
Cryo-EM structure of HACE2-bound SARS-cov-2 omicron spike protein with L371S, P373S and F375S mutations (local refinement)
Analyse Cryo-EM structure of HACE2-bound SARS-cov-2 omicron spike protein with L371S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YA1
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 4 · best druggability 0.67
Structure
electron microscopy · 2 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 56% helix, 3% strand | Q9BYF1 |
| B | Spike protein S1 | protein | 195 | 13% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.67 | 0.80 | 59 | empty |
| 2 | 349 | 0.65 | 0.80 | 38 | empty |
| 3 | 296 | 0.61 | 0.79 | 32 | empty |
| 4 | 54 | 0.27 | 0.73 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 789 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7YA1 · Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and… · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7YA1 · PDBe 7YA1 · UniProt Q9BYF1 · UniProt P0DTC2
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