MolNFT v2 · #214410 · protein
Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C (subparticle LLR-LRR)
8JN1 · Envelope protein (Fragment): “Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG…”. Electron microscopy at 3.5, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.79).…
- PDB
- 8JN1
- Type
- protein
- Length
- 1,935 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Dengue virus type 3; Homo sapiens
- Molecule
- Envelope protein (Fragment); Polyprotein; Human antibody DENV-115 heavy chain; Human…
- UniProt
- A0A173H1Z3, A0A330J7Q8
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · resolution 3.5 · 4 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope protein (Fragment) | protein | 493 | 20% helix, 30% strand | A0A173H1Z3 |
| B, D, F | Polyprotein | protein | 75 | 55% helix, 1% strand | A0A330J7Q8 |
| H | Human antibody DENV-115 heavy chain | protein | 122 | 2% helix, 41% strand | — |
| L | Human antibody DENV-115 light chain | protein | 109 | 3% helix, 36% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, E, H
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.79 | 0.81 | 113 | empty |
| 2 | 897 | 0.78 | 0.81 | 113 | empty |
| 3 | 934 | 0.75 | 0.78 | 96 | empty |
| 4 | 591 | 0.70 | 0.78 | 58 | empty |
| 5 | 280 | 0.68 | 0.83 | 41 | empty |
Interfaces
14 interfaces between chains.
- C–E · 1711 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1691 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1663 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1637 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1320 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 6 glycan (disulfide, N-glycosylation).
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 A0A173H1Z3
- Every structure of UniProt A0A330J7Q8
- Elsewhere: RCSB PDB 8JN1 · PDBe 8JN1 · UniProt A0A173H1Z3 · UniProt A0A330J7Q8
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