MolNFT v1 · #172484 · protein
Crystal structure of dengue 3 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8
7A3T · Core protein: “Crystal structure of dengue 3 virus envelope glycoprotein in complex with the Fab fragment of the broadly…”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 11 pockets (best druggability 0.60). MolNFT v1 #172484 on…
- PDB
- 7A3T
- Type
- protein
- Length
- 818 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein; EDE1 C8 antibody Fab fragment
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- A0A481XTQ0
- Ligands
- NAG, BMA, MAN, FUC, SO4
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 384 | 7% helix, 51% strand | A0A481XTQ0 |
| H | EDE1 C8 antibody Fab fragment | protein | 219 | 5% helix, 52% strand | — |
| L | EDE1 C8 antibody Fab fragment | protein | 215 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, H, L
- GOL · Glycerol · additive · 4 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.60 | 0.85 | 28 | empty |
| 2 | 258 | 0.52 | 0.75 | 37 | empty |
| 3 | 162 | 0.45 | 0.75 | 23 | empty |
| 4 | 130 | 0.45 | 0.77 | 15 | empty |
| 5 | 80 | 0.45 | 0.80 | 15 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1847 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 213 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7A3T · Crystal structure of dengue 3 virus envelope glycoprotein in complex with the Fab… · 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 A0A481XTQ0
- Elsewhere: RCSB PDB 7A3T · PDBe 7A3T · UniProt A0A481XTQ0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.