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Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11
Analyse Crystal structure of dengue 2 virus envelope glycoprotein in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UTB
- Type
- protein
- Length
- 1,632 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
- UniProt
- Q68Y26
- Ligands
- NAG, MAN, BMA, FUC, SO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein E | protein | 391 | 6% helix, 51% strand | Q68Y26 |
| B | Envelope glycoprotein E | protein | 390 | 7% helix, 51% strand | Q68Y26 |
| H | Broadly neutralizing human antibody EDE2 A11 | protein | 225 | 8% helix, 49% strand | — |
| I | Broadly neutralizing human antibody EDE2 A11 | protein | 203 | 6% helix, 47% strand | — |
| L | Broadly neutralizing human antibody EDE2 A11 | protein | 213 | 8% helix, 49% strand | — |
| M | Broadly neutralizing human antibody EDE2 A11 | protein | 210 | 9% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 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
- SO4 · Sulfate ion · ion · 2 copies · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.77 | 0.79 | 110 | empty |
| 2 | 788 | 0.74 | 0.79 | 81 | empty |
| 3 | 576 | 0.65 | 0.76 | 53 | empty |
| 4 | 547 | 0.63 | 0.76 | 59 | empty |
| 5 | 297 | 0.54 | 0.75 | 39 | NAG, FUC |
Interfaces
10 interfaces between chains.
- H–L · 2059 Ų buried · 27 hydrogen bonds · protein-protein
- I–M · 2024 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1958 Ų buried · 26 hydrogen bonds · protein-protein
- A–H · 568 Ų buried · 15 hydrogen bonds · protein-protein
- B–I · 558 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4UTB · 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 4UTB · PDBe 4UTB · UniProt Q68Y26
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