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The receptor binding domain of SARS-cov-2 omicron variant spike glycoprotein in complex with beta-55 and EY6A fabs
Analyse The receptor binding domain of SARS-cov-2 omicron variant spike glycoprotein in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QNW
- Type
- protein
- Length
- 1,057 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EY6A heavy chain; EY6A light chain; Surface glycoprotein; Beta-55 heavy chain; Beta-55…
- UniProt
- A0A7U3CI26
- Ligands
- NAG, CL
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | EY6A heavy chain | protein | 215 | 3% helix, 52% strand | — |
| L | EY6A light chain | protein | 212 | 6% helix, 51% strand | — |
| E | Surface glycoprotein | protein | 188 | 19% helix, 30% strand | A0A7U3CI26 |
| A | Beta-55 heavy chain | protein | 228 | 8% helix, 50% strand | — |
| B | Beta-55 light chain | protein | 214 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 9 copies · chains H, L, E, A, B
- ACT · Acetate ion · additive · 2 copies · chains E, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.64 | 0.74 | 62 | GOL |
| 2 | 241 | 0.60 | 0.80 | 42 | GOL |
| 3 | 409 | 0.57 | 0.74 | 53 | empty |
| 4 | 136 | 0.45 | 0.77 | 26 | empty |
| 5 | 52 | 0.40 | 0.82 | 21 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 2093 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1908 Ų buried · 12 hydrogen bonds · protein-protein
- E–A · 660 Ų buried · 10 hydrogen bonds · protein-protein
- H–E · 657 Ų buried · 15 hydrogen bonds · protein-protein
- L–E · 460 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7QNW · The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex… · 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 A0A7U3CI26
- Elsewhere: RCSB PDB 7QNW · PDBe 7QNW · UniProt A0A7U3CI26
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