Research workbench
Structural basis for enhanced infectivity and immune evasion of SARS- cov-2 variants
Analyse Structural basis for enhanced infectivity and immune evasion of SARS- cov-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N1Y
- Type
- protein
- Length
- 3,242 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1078 | 22% helix, 35% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1087 | 22% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1077 | 22% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 3 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 | 661 | 0.87 | 0.91 | 88 | empty |
| 2 | 468 | 0.79 | 0.87 | 61 | empty |
| 3 | 417 | 0.76 | 0.85 | 40 | empty |
| 4 | 419 | 0.76 | 0.85 | 30 | empty |
| 5 | 332 | 0.74 | 0.86 | 45 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5312 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 5289 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 4995 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7N1Y · Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants · 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 7N1Y · PDBe 7N1Y · UniProt P0DTC2
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