Research workbench
Structural basis of zika and dengue virus potent antibody cross- neutralization
Analyse Structural basis of zika and dengue virus potent antibody cross- neutralization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LBV
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E
- UniProt
- A0A120IIH9
- Ligands
- NAG, BMA, MAN, FUC, NA
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 390 | 7% helix, 51% strand | A0A120IIH9 |
| B | Envelope protein E | protein | 394 | 7% helix, 51% strand | A0A120IIH9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.56 | 0.76 | 33 | empty |
| 2 | 213 | 0.45 | 0.73 | 29 | empty |
| 3 | 108 | 0.37 | 0.74 | 15 | empty |
| 4 | 74 | 0.33 | 0.75 | 20 | empty |
| 5 | 88 | 0.32 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1387 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5LBV · Structural basis of zika and dengue virus potent antibody cross-neutralization · 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 A0A120IIH9
- Elsewhere: RCSB PDB 5LBV · PDBe 5LBV · UniProt A0A120IIH9
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