Research workbench
Cryo-EM structure of mature dengue virus 2 at 3.1 ångström resolution
Analyse Cryo-EM structure of mature dengue virus 2 at 3.1 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZQU
- Type
- protein
- Length
- 1,698 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- D0EPS0, O11875
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Genome polyprotein | protein | 494 | 22% helix, 38% strand | D0EPS0 |
| B, D, F | Genome polyprotein | protein | 72 | 54% helix, 0% strand | O11875 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.78 | 0.81 | 91 | empty |
| 2 | 949 | 0.78 | 0.80 | 102 | empty |
| 3 | 886 | 0.77 | 0.80 | 116 | empty |
| 4 | 195 | 0.65 | 0.84 | 36 | empty |
| 5 | 575 | 0.62 | 0.75 | 69 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1820 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1743 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1736 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1714 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1334 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZQU · Cryo-EM structure of mature Dengue virus 2 at 3.1 angstrom resolution · 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 D0EPS0
- Every structure of UniProt O11875
- Elsewhere: RCSB PDB 6ZQU · PDBe 6ZQU · UniProt D0EPS0 · UniProt O11875
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