Research workbench
Cryo-EM structure of prefusion SARS-cov-2 spike omicron B.1.1.529 variant
Analyse Cryo-EM structure of prefusion SARS-cov-2 spike omicron B.1.1.529 variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7THK
- Type
- protein
- Length
- 2,925 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 0.85
Structure
electron microscopy · 3 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 860 | 26% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1043 | 22% helix, 33% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1022 | 22% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, C, B
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 | 912 | 0.85 | 0.87 | 105 | empty |
| 2 | 369 | 0.84 | 0.92 | 40 | empty |
| 3 | 1137 | 0.83 | 0.84 | 117 | empty |
| 4 | 755 | 0.82 | 0.86 | 89 | empty |
| 5 | 216 | 0.80 | 0.94 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6187 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 5901 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4862 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7THK · Cryo-EM structure of prefusion SARS-CoV-2 spike omicron B.1.1.529 variant · 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 7THK · PDBe 7THK · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.