MolNFT v1 · #107991 · protein
Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8
4UTA · Envelope glycoprotein E: “Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly…”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 19 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 4UTA
- Type
- protein
- Length
- 1,619 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E; Broadly neutralizing human antibody EDE1 C8 heavy chain; Broadly…
- UniProt
- Q68Y26
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein E | protein | 373 | 7% helix, 51% strand | Q68Y26 |
| B | Envelope glycoprotein E | protein | 386 | 7% helix, 50% strand | Q68Y26 |
| H | Broadly neutralizing human antibody EDE1 C8 heavy chain | protein | 221 | 6% helix, 50% strand | — |
| I | Broadly neutralizing human antibody EDE1 C8 heavy chain | protein | 211 | 6% helix, 52% strand | — |
| L | Broadly neutralizing human antibody EDE1 C8 light chain | protein | 215 | 6% helix, 49% strand | — |
| M | Broadly neutralizing human antibody EDE1 C8 light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, I, B, H
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains I, H
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B, H
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.82 | 0.83 | 89 | empty |
| 2 | 1089 | 0.78 | 0.80 | 103 | empty |
| 3 | 241 | 0.59 | 0.80 | 41 | empty |
| 4 | 263 | 0.59 | 0.79 | 39 | empty |
| 5 | 58 | 0.52 | 0.88 | 20 | empty |
Interfaces
11 interfaces between chains.
- I–M · 1796 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1790 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1690 Ų buried · 22 hydrogen bonds · protein-protein
- B–H · 545 Ų buried · 7 hydrogen bonds · protein-protein
- A–I · 532 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4UTA · Crystal structure of dengue 2 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 Q68Y26
- Elsewhere: RCSB PDB 4UTA · PDBe 4UTA · UniProt Q68Y26
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