Research workbench
Structural basis for human coronavirus attachment to sialic acid receptors
Analyse Structural basis for human coronavirus attachment to sialic acid receptors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NZK
- Type
- protein
- Length
- 3,525 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike surface glycoprotein
- UniProt
- Q696P8
- Ligands
- MJJ, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike surface glycoprotein | protein | 1175 | 23% helix, 35% strand | Q696P8 |
Ligands and binding sites
- MJJ · methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 75 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 21 copies · chains B, C, A
- MAN · alpha-D-mannopyranose · sugar · 6 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 | 660 | 0.85 | 0.89 | 100 | empty |
| 2 | 165 | 0.83 | 0.98 | 27 | empty |
| 3 | 500 | 0.83 | 0.90 | 51 | empty |
| 4 | 791 | 0.83 | 0.86 | 90 | empty |
| 5 | 170 | 0.83 | 0.97 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6125 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 6117 Ų buried · 73 hydrogen bonds · protein-protein
- A–C · 6112 Ų buried · 73 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 6NZK · Structural basis for human coronavirus attachment to sialic acid receptors · 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 Q696P8
- Elsewhere: RCSB PDB 6NZK · PDBe 6NZK · UniProt Q696P8
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