Research workbench
Cryoem structure of dengue virus
Analyse Cryoem structure of dengue virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J27
- Type
- protein
- Length
- 1,701 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Small envelope protein M
- UniProt
- P14340
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 23% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope protein E | protein | 495 | 19% helix, 25% strand | P14340 |
| B, D, F | Small envelope protein M | protein | 72 | 56% helix, 1% strand | P14340 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.88 | 0.89 | 127 | empty |
| 2 | 736 | 0.79 | 0.83 | 85 | empty |
| 3 | 1000 | 0.79 | 0.81 | 96 | empty |
| 4 | 620 | 0.70 | 0.78 | 54 | empty |
| 5 | 414 | 0.61 | 0.77 | 55 | empty |
Interfaces
9 interfaces between chains.
- C–E · 1680 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1573 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1539 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1504 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1086 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 3J27 · CryoEM structure of Dengue virus · 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 P14340
- Elsewhere: RCSB PDB 3J27 · PDBe 3J27 · UniProt P14340
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