Research workbench
Crystal structure of the precursor membrane protein- envelope protein heterodimer from the dengue 2 virus at low pH
Analyse Crystal structure of the precursor membrane protein- envelope protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5X
- 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
- SHD, NAG, BMA, NDG
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 390 | 8% helix, 48% strand | O09234 |
| C | Prm | protein | 81 | 4% helix, 57% strand | O09234 |
Ligands and binding sites
- SHD · alpha-D-altropyranose · ligand
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.59 | 0.91 | 19 | empty |
| 2 | 77 | 0.41 | 0.79 | 19 | empty |
| 3 | 57 | 0.39 | 0.80 | 13 | empty |
| 4 | 58 | 0.36 | 0.79 | 19 | empty |
| 5 | 109 | 0.35 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–C · 857 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3C5X · 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 3C5X · PDBe 3C5X · UniProt O09234
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