Research workbench
SARS-cov-2 S B.1.1.529 omicron variant (rbd + S309 local refinement)
Analyse SARS-cov-2 S B.1.1.529 omicron variant (rbd + S309 local refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TLY
- Type
- protein
- Length
- 408 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S309 Fab heavy chain; S309 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC
- Pockets
- 3 · best druggability 0.51
Structure
electron microscopy · 3 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S309 Fab heavy chain | protein | 126 | 7% helix, 50% strand | — |
| B | S309 Fab light chain | protein | 101 | 3% helix, 47% strand | — |
| I | Spike glycoprotein | protein | 181 | 15% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, I
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.51 | 0.74 | 40 | NAG, FUC |
| 2 | 62 | 0.38 | 0.79 | 16 | empty |
| 3 | 87 | 0.34 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 735 Ų buried · 6 hydrogen bonds · protein-protein
- A–I · 659 Ų buried · 8 hydrogen bonds · protein-protein
- B–I · 180 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TLY · SARS-CoV-2 S B.1.1.529 Omicron variant (RBD + S309 Local Refinement) · 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
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7TLY · PDBe 7TLY · UniProt P0DTC2
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