Research workbench
Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprotein with domain 0 in the proximal conformation
Analyse Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprotein with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7US6
- Type
- protein
- Length
- 3,159 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- unidentified human coronavirus
- Molecule
- Spike glycoprotein
- UniProt
- A0A8E6CMP0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.8 · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1053 | 23% helix, 35% strand | A0A8E6CMP0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 89 copies · chains A, C, B
- 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 | 1039 | 0.81 | 0.83 | 108 | empty |
| 2 | 296 | 0.81 | 0.92 | 55 | empty |
| 3 | 1051 | 0.81 | 0.82 | 125 | empty |
| 4 | 811 | 0.80 | 0.83 | 102 | empty |
| 5 | 230 | 0.79 | 0.92 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4145 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 4082 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 3965 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7US6 · Structure of the human coronavirus ccov-hupn-2018 spike glycoprotein with domain 0 in the… · 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 A0A8E6CMP0
- Elsewhere: RCSB PDB 7US6 · PDBe 7US6 · UniProt A0A8E6CMP0
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