MolNFT v1 · #147849 · protein
Crystal structure of the precursor membrane protein-envelope protein heterodimer from the yellow fever virus
6EPK · Envelope protein E: “Crystal structure of the precursor membrane protein-envelope protein heterodimer from the yellow fever virus”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 14 pockets (best druggability 0.74). MolNFT v1 #147849…
- PDB
- 6EPK
- Type
- protein
- Length
- 974 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Precursor membrane protein
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- Q6DV88
- Ligands
- NAG, MAN, BMA, FUC, SO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Envelope protein E (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 407 | 8% helix, 50% strand | Q6DV88 |
| B, E | Precursor membrane protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 80 | 4% helix, 54% strand | Q6DV88 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, E
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B, E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, E
- SO4 · Sulfate ion · ion · 23 copies · chains A, B, D, E
- GOL · Glycerol · additive · 13 copies · chains A, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.74 | 0.80 | 65 | GOL |
| 2 | 121 | 0.46 | 0.78 | 21 | GOL |
| 3 | 130 | 0.45 | 0.77 | 22 | SO4, GOL |
| 4 | 141 | 0.43 | 0.75 | 20 | empty |
| 5 | 115 | 0.43 | 0.77 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 885 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 884 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 458 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 436 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 158 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6EPK · Crystal structure of the precursor membrane protein-envelope protein heterodimer from the… · 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 Q6DV88
- Elsewhere: RCSB PDB 6EPK · PDBe 6EPK · UniProt Q6DV88
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