Research workbench
SARS-cov-2 omicron 1-rbd down spike protein trimer without the P986- P987 stabilizing mutations (S-gsas-omicron)
Analyse SARS-cov-2 omicron 1-rbd down spike protein trimer without the P986- P987… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TGE
- Type
- protein
- Length
- 2,677 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1030 | 22% helix, 31% strand | — |
| B | Spike glycoprotein | protein | 842 | 25% helix, 31% strand | — |
| C | Spike glycoprotein | protein | 805 | 24% helix, 31% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 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 | 867 | 0.85 | 0.87 | 88 | empty |
| 2 | 243 | 0.82 | 0.94 | 30 | empty |
| 3 | 587 | 0.81 | 0.87 | 84 | empty |
| 4 | 365 | 0.80 | 0.90 | 34 | empty |
| 5 | 299 | 0.80 | 0.91 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5481 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 4498 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 4451 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 7TGE · SARS-CoV-2 Omicron 1-RBD down Spike Protein Trimer without the P986-P987 stabilizing… · 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
- Elsewhere: RCSB PDB 7TGE · PDBe 7TGE
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.