Research workbench
Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain
Analyse Cryo-EM structure of the prefusion state of canine distemper virus fusion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XYE
- Type
- protein
- Length
- 1,293 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.3
- Source
- Canine morbillivirus
- Molecule
- Fusion glycoprotein F2; Fusion glycoprotein F1
- UniProt
- Q9YKL7
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 4.3 · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Fusion glycoprotein F2 | protein | 74 | 43% helix, 23% strand | Q9YKL7 |
| B, D, F | Fusion glycoprotein F1 | protein | 357 | 25% helix, 23% strand | Q9YKL7 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.78 | 0.82 | 113 | empty |
| 2 | 1156 | 0.78 | 0.79 | 113 | empty |
| 3 | 465 | 0.73 | 0.82 | 56 | empty |
| 4 | 555 | 0.69 | 0.78 | 71 | empty |
| 5 | 390 | 0.69 | 0.81 | 38 | empty |
Interfaces
12 interfaces between chains.
- E–F · 4177 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 4174 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 4163 Ų buried · 44 hydrogen bonds · protein-protein
- B–F · 2203 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 2177 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6XYE · Cryo-EM structure of the prefusion state of canine distemper virus fusion protein… · 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 Q9YKL7
- Elsewhere: RCSB PDB 6XYE · PDBe 6XYE · UniProt Q9YKL7
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