MolNFT v1 · #165818 · protein
Cryo-EM structure of the hcov-229E spike glycoprotein
6U7H: “Cryo-EM structure of the hcov-229E spike glycoprotein”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.90). MolNFT v1 #165818 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6U7H
- Type
- protein
- Length
- 2,895 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 965 | 23% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, C
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 | 1116 | 0.90 | 0.92 | 155 | empty |
| 2 | 652 | 0.79 | 0.84 | 70 | empty |
| 3 | 697 | 0.79 | 0.84 | 77 | empty |
| 4 | 821 | 0.79 | 0.82 | 93 | empty |
| 5 | 794 | 0.79 | 0.82 | 94 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4532 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 4530 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 4519 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6U7H · Cryo-EM structure of the HCoV-229E spike glycoprotein · 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
- Elsewhere: RCSB PDB 6U7H · PDBe 6U7H
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