MolNFT v1 · #127561 · protein
Crystal structure of A259C covalently linked dengue 2 virus envelope glycoprotein dimer in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11
5N0A · Envelope glycoprotein E: “Crystal structure of A259C covalently linked dengue 2 virus envelope glycoprotein dimer in complex with the…”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 13 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5N0A
- Type
- protein
- Length
- 1,234 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E; Broadly neutralizing human antibody EDE2 A11 heavy chain…
- UniProt
- Q68Y26
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein E | protein | 373 | 6% helix, 50% strand | Q68Y26 |
| B | Envelope glycoprotein E | protein | 379 | 6% helix, 51% strand | Q68Y26 |
| H, I | Broadly neutralizing human antibody EDE2 A11 heavy chain | protein | 131 | 7% helix, 47% strand | — |
| L, M | Broadly neutralizing human antibody EDE2 A11 | protein | 110 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, I, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains I, M, H, L
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains I, M, H, L
- 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
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.73 | 0.78 | 94 | empty |
| 2 | 833 | 0.73 | 0.78 | 78 | empty |
| 3 | 255 | 0.54 | 0.76 | 34 | NAG |
| 4 | 131 | 0.54 | 0.82 | 32 | empty |
| 5 | 290 | 0.54 | 0.75 | 39 | NAG |
Interfaces
10 interfaces between chains.
- A–B · 1882 Ų buried · 15 hydrogen bonds · protein-protein
- I–M · 1072 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1068 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 528 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 520 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5N0A · Crystal structure of A259C covalently linked dengue 2 virus envelope glycoprotein dimer… · 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 5N0A · PDBe 5N0A · UniProt Q68Y26
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.