Research workbench
SARS-cov-2 omicron variant spike rbd in complex with Fab XGV282
Analyse SARS-cov-2 omicron variant spike rbd 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
- 7WLC
- Type
- protein
- Length
- 430 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Heavy chain of XGV282; Light chain of XGV282
- UniProt
- P0DTC2
- Pockets
- 7 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 201 | 11% helix, 21% strand | P0DTC2 |
| H | Heavy chain of XGV282 | protein | 118 | 5% helix, 49% strand | — |
| L | Light chain of XGV282 | protein | 111 | 0% helix, 47% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.78 | 0.97 | 29 | empty |
| 2 | 309 | 0.56 | 0.76 | 55 | empty |
| 3 | 166 | 0.55 | 0.80 | 21 | empty |
| 4 | 100 | 0.41 | 0.77 | 22 | empty |
| 5 | 69 | 0.30 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 879 Ų buried · 4 hydrogen bonds · protein-protein
- E–H · 523 Ų buried · 1 hydrogen bond · protein-protein
- E–L · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7WLC · SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv282 · the same entry in another collection · chain E against E, 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 7WLC · PDBe 7WLC · UniProt P0DTC2
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