MolNFT v1 · #107993 · protein
Crystal structure of dengue 2 virus envelope glycoprotein
4UTC · Envelope glycoprotein E: “Crystal structure of dengue 2 virus envelope glycoprotein”. X-ray diffraction, 3 ligands (NAG, BMA, FUC), 10 pockets (best druggability 0.69). MolNFT v1 #107993 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4UTC
- Type
- protein
- Length
- 781 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E
- UniProt
- Q68Y26
- Ligands
- NAG, BMA, FUC
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein E | protein | 391 | 6% helix, 50% strand | Q68Y26 |
| B | Envelope glycoprotein E | protein | 390 | 6% helix, 50% strand | Q68Y26 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.69 | 0.96 | 12 | empty |
| 2 | 378 | 0.62 | 0.78 | 43 | empty |
| 3 | 242 | 0.56 | 0.78 | 33 | empty |
| 4 | 121 | 0.50 | 0.80 | 32 | empty |
| 5 | 84 | 0.49 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1794 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4UTC · Crystal structure of dengue 2 virus envelope glycoprotein · 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 Q68Y26
- Elsewhere: RCSB PDB 4UTC · PDBe 4UTC · UniProt Q68Y26
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