Research workbench
Structure of dengue virus diii in complex with Fab 2H12
Analyse Structure of dengue virus diii in complex with Fab 2H12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AL8
- Type
- protein
- Length
- 523 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein; Fab 2H12 heavy chain; Fab 2H12 light chain
- UniProt
- Q8BE57
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Envelope protein | protein | 98 | 0% helix, 44% strand | Q8BE57 |
| H | Fab 2H12 heavy chain | protein | 212 | 10% helix, 52% strand | — |
| L | Fab 2H12 light chain | protein | 213 | 6% helix, 49% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.60 | 0.75 | 56 | GOL |
| 2 | 233 | 0.59 | 0.80 | 30 | empty |
| 3 | 78 | 0.33 | 0.75 | 17 | empty |
| 4 | 73 | 0.33 | 0.75 | 19 | empty |
| 5 | 77 | 0.32 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1776 Ų buried · 19 hydrogen bonds · protein-protein
- C–H · 415 Ų buried · 8 hydrogen bonds · protein-protein
- C–L · 335 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4AL8 · Structure of Dengue virus DIII in complex with Fab 2H12 · the same entry in another collection · chain C against C, 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 Q8BE57
- Elsewhere: RCSB PDB 4AL8 · PDBe 4AL8 · UniProt Q8BE57
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