MolNFT v1 · #17161 · protein
Crystal structure of the dengue 2 virus envelope protein in complex with N-octyl-beta-D-glucoside
1OKE · Major envelope protein E: “Crystal structure of the dengue 2 virus envelope protein in complex with N-octyl-beta-D-glucoside”. X-ray diffraction, 3 ligands (NAG, BMA, FUL), 12 pockets (best druggability 0.68). MolNFT v1 #17161 on…
- PDB
- 1OKE
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major envelope protein E
- UniProt
- P12823
- Ligands
- NAG, BMA, FUL
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Major envelope protein E | protein | 394 | 6% helix, 49% 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
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.68 | 0.84 | 31 | BOG |
| 2 | 220 | 0.65 | 0.83 | 29 | BOG |
| 3 | 313 | 0.64 | 0.80 | 49 | empty |
| 4 | 297 | 0.64 | 0.81 | 45 | empty |
| 5 | 162 | 0.43 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2042 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1OKE · Crystal structure of the dengue 2 virus envelope protein in complex with… · 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 1OKE · PDBe 1OKE · UniProt P12823
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