Research workbench
Cryo-EM structure of PDF-2180 Spike glycoprotein
Analyse Cryo-EM structure of PDF-2180 Spike glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U6R
- Type
- protein
- Length
- 3,291 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Bat coronavirus
- Molecule
- PDF-2180 Spike glycoprotein
- UniProt
- A0A1W6ASU7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 2.5 · 1 distinct chain · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | PDF-2180 Spike glycoprotein | protein | 1097 | 24% helix, 34% strand | A0A1W6ASU7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 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 | 1076 | 0.88 | 0.89 | 124 | empty |
| 2 | 741 | 0.86 | 0.89 | 99 | empty |
| 3 | 376 | 0.84 | 0.92 | 69 | empty |
| 4 | 418 | 0.83 | 0.91 | 78 | empty |
| 5 | 423 | 0.82 | 0.90 | 74 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5313 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 5301 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 5299 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 45 glycan (disulfide, N-glycosylation).
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 A0A1W6ASU7
- Elsewhere: RCSB PDB 7U6R · PDBe 7U6R · UniProt A0A1W6ASU7
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