Research workbench
Cryoem structure of eastern equine encephalitis (eeev) vlp
Analyse Cryoem structure of eastern equine encephalitis (eeev) vlp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XO4
- Type
- protein
- Length
- 3,992 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Togavirin
- EC
- 3.4.21.90
- UniProt
- Q88678
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Togavirin (EC 3.4.21.90) | protein | 433 | 13% helix, 34% strand | Q88678 |
| B, E, H, K | Togavirin (EC 3.4.21.90) | protein | 414 | 14% helix, 36% strand | Q88678 |
| C, F, I, L | Togavirin (EC 3.4.21.90) | protein | 151 | 2% helix, 28% strand | Q88678 |
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 | 1112 | 0.83 | 0.84 | 121 | empty |
| 2 | 1058 | 0.83 | 0.84 | 114 | empty |
| 3 | 1122 | 0.83 | 0.84 | 101 | empty |
| 4 | 235 | 0.74 | 0.89 | 38 | empty |
| 5 | 517 | 0.73 | 0.82 | 77 | empty |
Interfaces
23 interfaces between chains.
- G–H · 2950 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2929 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2927 Ų buried · 21 hydrogen bonds · protein-protein
- J–K · 2915 Ų buried · 17 hydrogen bonds · protein-protein
- E–J · 632 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 6XO4 · CryoEM structure of Eastern Equine Encephalitis (EEEV) 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 Q88678
- Elsewhere: RCSB PDB 6XO4 · PDBe 6XO4 · UniProt Q88678
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