Research workbench
Cryo-EM structure of apo SARS-cov-2 omicron spike protein (S-2P-gsas)
Analyse Cryo-EM structure of apo SARS-cov-2 omicron spike protein (S-2P-gsas) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y9S
- Type
- protein
- Length
- 3,126 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 0.88
Structure
electron microscopy · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1041 | 21% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1044 | 21% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 53 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.88 | 0.90 | 100 | empty |
| 2 | 732 | 0.84 | 0.88 | 84 | empty |
| 3 | 1055 | 0.84 | 0.84 | 85 | empty |
| 4 | 647 | 0.83 | 0.88 | 66 | empty |
| 5 | 950 | 0.77 | 0.79 | 90 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5050 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4834 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4332 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 37 glycan (disulfide, N-glycosylation).
Compared structures
- 7Y9S · Cryo-EM structure of apo SARS-CoV-2 Omicron spike protein (S-2P-GSAS) · 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 7Y9S · PDBe 7Y9S · UniProt P0DTC2
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