Research workbench
SARS-cov-2 omicron variant spike protein in complex with Fab XGV282
Analyse SARS-cov-2 omicron variant spike protein in complex with Fab XGV282 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WE7
- Type
- protein
- Length
- 3,981 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab 282; The light chain of Fab 282; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J, K | Heavy chain of Fab 282 | protein | 118 | 3% helix, 37% strand | — |
| L, M, N | The light chain of Fab 282 | protein | 111 | 3% helix, 47% strand | — |
| D, E, G | Spike glycoprotein | protein | 1098 | 21% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 copies · chains D, E, G
- BMA · beta-D-mannopyranose · sugar · 5 copies
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 | 800 | 0.84 | 0.87 | 92 | empty |
| 2 | 475 | 0.83 | 0.89 | 49 | empty |
| 3 | 462 | 0.81 | 0.89 | 59 | empty |
| 4 | 334 | 0.81 | 0.91 | 50 | empty |
| 5 | 916 | 0.81 | 0.83 | 92 | empty |
Interfaces
15 interfaces between chains.
- D–E · 5768 Ų buried · 33 hydrogen bonds · protein-protein
- D–G · 5647 Ų buried · 45 hydrogen bonds · protein-protein
- E–G · 4932 Ų buried · 27 hydrogen bonds · protein-protein
- K–N · 923 Ų buried · 11 hydrogen bonds · protein-protein
- J–M · 920 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 44 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7WE7 · SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv282 · the same entry in another collection · chain H against H, 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 7WE7 · PDBe 7WE7 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.