Research workbench
Structure of dengue virus ediii in complex with Fab 3E31
Analyse Structure of dengue virus ediii in complex with Fab 3E31 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BZ1
- Type
- protein
- Length
- 526 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein; Fab 3E31 heavy chain; Fab 3E31 light chain
- UniProt
- Q7TGC7
- Ligands
- NA, ZN, CL
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein | protein | 96 | 3% helix, 53% strand | Q7TGC7 |
| H | Fab 3E31 heavy chain | protein | 212 | 8% helix, 53% strand | — |
| L | Fab 3E31 light chain | protein | 218 | 6% helix, 53% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains H, L
- ZN · Zinc ion · metal · chains L
- CL · Chloride ion · ion · 2 copies · chains L
- GOL · Glycerol · additive · 2 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.58 | 0.76 | 32 | empty |
| 2 | 211 | 0.53 | 0.77 | 33 | empty |
| 3 | 71 | 0.53 | 0.86 | 21 | NA |
| 4 | 338 | 0.52 | 0.73 | 47 | empty |
| 5 | 78 | 0.32 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1760 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 396 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 322 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4BZ1 · Structure of dengue virus EDIII in complex with Fab 3e31 · 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 Q7TGC7
- Elsewhere: RCSB PDB 4BZ1 · PDBe 4BZ1 · UniProt Q7TGC7
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