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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
- 5LCV
- Type
- protein
- Length
- 1,249 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein; Broadly neutralizing human antibody EDE2 A11
- UniProt
- A0A120IIH9
- Ligands
- NAG, BMA, FUC
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein | protein | 406 | 7% helix, 50% strand | A0A120IIH9 |
| B | Polyprotein | protein | 405 | 7% helix, 48% strand | A0A120IIH9 |
| H | Broadly neutralizing human antibody EDE2 A11 | protein | 226 | 7% helix, 49% strand | — |
| L | Broadly neutralizing human antibody EDE2 A11 | protein | 212 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, H, A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.67 | 0.77 | 50 | empty |
| 2 | 483 | 0.59 | 0.74 | 52 | empty |
| 3 | 341 | 0.56 | 0.75 | 47 | NAG |
| 4 | 243 | 0.49 | 0.74 | 26 | empty |
| 5 | 68 | 0.36 | 0.77 | 13 | empty |
Interfaces
5 interfaces between chains.
- H–L · 2000 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1525 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 560 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 150 Ų buried · 1 hydrogen bond · protein-protein
- A–L · 108 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5LCV · Structural basis of Zika and Dengue virus potent antibody cross-neutralization · the same entry in another collection · chain H against H, 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 5LCV · PDBe 5LCV · UniProt A0A120IIH9
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