Research workbench
Crystal structure of the dengue 2 virus envelope protein
Analyse Crystal structure of the dengue 2 virus envelope protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OAN
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein
- UniProt
- P12823
- Ligands
- NAG, BMA, FUC, NA
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Envelope glycoprotein | protein | 394 | 6% helix, 46% strand | P12823 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.67 | 0.76 | 74 | empty |
| 2 | 519 | 0.65 | 0.77 | 61 | empty |
| 3 | 60 | 0.55 | 0.88 | 17 | empty |
| 4 | 53 | 0.54 | 0.89 | 17 | empty |
| 5 | 119 | 0.48 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1669 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1OAN · Crystal structure of the dengue 2 virus envelope protein · 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 P12823
- Elsewhere: RCSB PDB 1OAN · PDBe 1OAN · UniProt P12823
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