Research workbench
Structure of a redesigned cross-reactive antibody to dengue virus with increased in vivo potency
Analyse Structure of a redesigned cross-reactive antibody to dengue virus with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AAW
- Type
- protein
- Length
- 1,941 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SCFV513; Dengue serotype 4 envelope protein domain 3
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, H, K | SCFV513 | protein | 228 | 4% helix, 49% strand | — |
| B | SCFV513 | protein | 229 | 4% helix, 51% strand | — |
| C, E, I, J, L | Dengue serotype 4 envelope protein domain 3 | protein | 96 | 0% helix, 45% strand | — |
| F | SCFV513 | protein | 227 | 4% helix, 50% strand | — |
| G | Dengue serotype 4 envelope protein domain 3 | protein | 93 | 0% helix, 40% strand | — |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.79 | 0.81 | 115 | empty |
| 2 | 1041 | 0.79 | 0.81 | 119 | empty |
| 3 | 840 | 0.75 | 0.79 | 83 | empty |
| 4 | 291 | 0.67 | 0.83 | 46 | empty |
| 5 | 199 | 0.61 | 0.82 | 44 | empty |
Interfaces
18 interfaces between chains.
- D–E · 1051 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 1043 Ų buried · 21 hydrogen bonds · protein-protein
- B–J · 1029 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 997 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 994 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5AAW · Structure of a redesigned cross-reactive antibody to dengue virus with increased in vivo… · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 5AAW · PDBe 5AAW
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