Research workbench
SARS-cov-2 omicron BA.2 rbd in complex with covox-150 Fab
Analyse SARS-cov-2 omicron BA.2 rbd in complex with covox-150 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZF8
- Type
- protein
- Length
- 626 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Covox-150 heavy chain; Covox-150 light chain; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Covox-150 heavy chain | protein | 216 | 10% helix, 53% strand | — |
| L | Covox-150 light chain | protein | 215 | 5% helix, 48% strand | — |
| E | Spike protein S1 | protein | 195 | 16% helix, 31% strand | P0DTC2 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.55 | 0.77 | 37 | empty |
| 2 | 358 | 0.53 | 0.73 | 44 | empty |
| 3 | 77 | 0.46 | 0.82 | 18 | empty |
| 4 | 79 | 0.45 | 0.82 | 18 | empty |
| 5 | 113 | 0.36 | 0.73 | 28 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1744 Ų buried · 9 hydrogen bonds · protein-protein
- H–E · 812 Ų buried · 22 hydrogen bonds · protein-protein
- L–E · 376 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7ZF8 · SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab · 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 7ZF8 · PDBe 7ZF8 · UniProt P0DTC2
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