Research workbench
Electron cryo-microscopy of "immature" Chikungunya VLP
Analyse Electron cryo-microscopy of "immature" Chikungunya VLP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VU2
- Type
- protein
- Length
- 4,236 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 6.8
- Source
- Chikungunya virus (strain 37997); Chikungunya virus strain Senegal 37997
- Molecule
- E1 envelope glycoprotein; E3 envelope glycoprotein; capsid protein; E2 envelope…
- UniProt
- A0A0H4CWF2, C7S7A1, Q5XXP3
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 6.8 · 6 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, N, O, P | E1 envelope glycoprotein | protein | 382 | 5% helix, 50% strand | A0A0H4CWF2 |
| A, B, C, D | E1 envelope glycoprotein | protein | 341 | 3% helix, 50% strand | A0A0H4CWF2 |
| U, V, W, X | E3 envelope glycoprotein | protein | 60 | 37% helix, 13% strand | C7S7A1 |
| I, J, K, L | capsid protein | protein | 149 | 7% helix, 50% strand | Q5XXP3 |
| E, F, G, H | E1 envelope glycoprotein | protein | 46 | 63% helix, 0% strand | Q5XXP3 |
| Q, R, S, T | E2 envelope glycoprotein | protein | 81 | 46% helix, 0% strand | Q5XXP3 |
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 | 961 | 0.85 | 0.86 | 100 | empty |
| 2 | 552 | 0.79 | 0.86 | 70 | empty |
| 3 | 683 | 0.79 | 0.84 | 55 | empty |
| 4 | 633 | 0.76 | 0.82 | 76 | empty |
| 5 | 366 | 0.74 | 0.85 | 50 | empty |
Interfaces
42 interfaces between chains.
- C–O · 2094 Ų buried · 30 hydrogen bonds · protein-protein
- M–A · 2079 Ų buried · 32 hydrogen bonds · protein-protein
- D–P · 2078 Ų buried · 30 hydrogen bonds · protein-protein
- B–N · 2074 Ų buried · 32 hydrogen bonds · protein-protein
- A–U · 1078 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 68 disulfide (disulfide).
Compared structures
- 5VU2 · Electron cryo-microscopy of "immature" chikungunya vlp · 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 A0A0H4CWF2
- Every structure of UniProt C7S7A1
- Every structure of UniProt Q5XXP3
- Elsewhere: RCSB PDB 5VU2 · PDBe 5VU2 · UniProt A0A0H4CWF2 · UniProt C7S7A1 · UniProt Q5XXP3
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