Research workbench
Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 B7
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
- 4UT6
- Type
- protein
- Length
- 1,258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein E; Broadly neutralizing human antibody EDE2 B7; Broadly…
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein E | protein | 394 | 5% helix, 50% strand | — |
| B | Envelope glycoprotein E | protein | 391 | 5% helix, 49% strand | — |
| H, I | Broadly neutralizing human antibody EDE2 B7 | protein | 130 | 7% helix, 47% strand | — |
| L | Broadly neutralizing human antibody EDE2 | protein | 106 | 7% helix, 42% strand | — |
| M | Broadly neutralizing human antibody EDE2 | protein | 107 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.77 | 0.79 | 104 | empty |
| 2 | 1197 | 0.74 | 0.77 | 106 | empty |
| 3 | 152 | 0.53 | 0.80 | 31 | empty |
| 4 | 220 | 0.51 | 0.76 | 40 | NAG |
| 5 | 125 | 0.51 | 0.80 | 28 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1880 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1121 Ų buried · 13 hydrogen bonds · protein-protein
- I–M · 1120 Ų buried · 14 hydrogen bonds · protein-protein
- B–I · 572 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 566 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4UT6 · 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
- Elsewhere: RCSB PDB 4UT6 · PDBe 4UT6
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