MolNFT v1 · #59715 · protein
Crystal structure of the precursor membrane protein- envelope protein heterodimer from the dengue 2 virus at neutral pH
3C6E · Envelope protein E: “Crystal structure of the precursor membrane protein- envelope protein heterodimer from the dengue 2 virus at…”. X-ray diffraction, 3 ligands (NAG, NDG, MAN), 4 pockets (best druggability 0.53). MolNFT v1 #59715…
- PDB
- 3C6E
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Prm
- UniProt
- O09234
- Ligands
- NAG, NDG, MAN
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 390 | 6% helix, 45% strand | O09234 |
| C | Prm | protein | 81 | 4% helix, 56% strand | O09234 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains C
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.53 | 0.84 | 28 | empty |
| 2 | 95 | 0.45 | 0.79 | 19 | empty |
| 3 | 121 | 0.40 | 0.75 | 24 | empty |
| 4 | 79 | 0.37 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–C · 857 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3C6E · Crystal structure of the precursor membrane protein- envelope protein heterodimer from… · 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 O09234
- Elsewhere: RCSB PDB 3C6E · PDBe 3C6E · UniProt O09234
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