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
- 4ALA
- Type
- protein
- Length
- 498 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
- Q7TGD1
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Envelope protein | protein | 78 | 0% helix, 40% strand | Q7TGD1 |
| H | Fab 2H12 heavy chain | protein | 208 | 7% helix, 52% strand | — |
| L | Fab 2H12 light chain | protein | 212 | 6% helix, 51% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains H, L, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.60 | 0.78 | 39 | GOL |
| 2 | 351 | 0.58 | 0.76 | 49 | GOL |
| 3 | 70 | 0.33 | 0.76 | 14 | empty |
| 4 | 84 | 0.31 | 0.73 | 15 | empty |
| 5 | 63 | 0.28 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1756 Ų buried · 20 hydrogen bonds · protein-protein
- C–H · 323 Ų buried · 7 hydrogen bonds · protein-protein
- C–L · 322 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4ALA · 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 Q7TGD1
- Elsewhere: RCSB PDB 4ALA · PDBe 4ALA · UniProt Q7TGD1
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