Research workbench
Cryo-EM structure of the SARS-cov-2 omicron spike protein
Analyse Cryo-EM structure of the SARS-cov-2 omicron spike protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T9J
- Type
- protein
- Length
- 2,703 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 835 | 24% helix, 36% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 836 | 24% helix, 37% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1032 | 21% helix, 35% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.87 | 0.90 | 121 | empty |
| 2 | 434 | 0.85 | 0.92 | 64 | empty |
| 3 | 649 | 0.78 | 0.83 | 87 | empty |
| 4 | 511 | 0.77 | 0.85 | 46 | empty |
| 5 | 725 | 0.77 | 0.82 | 76 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5115 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 4549 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4479 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 glycan, 34 disulfide (N-glycosylation, disulfide).
Compared structures
- 7T9J · Cryo-EM structure of the SARS-CoV-2 Omicron spike protein · the same entry in another collection · chain A against A, TM-score 1.00
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 P0DTC2
- Elsewhere: RCSB PDB 7T9J · PDBe 7T9J · UniProt P0DTC2
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