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
- 5AAM
- Type
- protein
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SCFV513; Envelope protein
- UniProt
- U3N5N6
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SCFV513 | protein | 228 | 3% helix, 49% strand | — |
| B | SCFV513 | protein | 227 | 3% helix, 49% strand | — |
| C | Envelope protein | protein | 95 | 0% helix, 36% strand | U3N5N6 |
| J | Envelope protein | protein | 96 | 0% helix, 43% strand | U3N5N6 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.77 | 0.79 | 125 | empty |
Interfaces
4 interfaces between chains.
- B–J · 1090 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1073 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 2 hydrogen bonds · protein-protein
- A–J · 73 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5AAM · Structure of a redesigned cross-reactive antibody to dengue virus with increased in vivo… · 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 U3N5N6
- Elsewhere: RCSB PDB 5AAM · PDBe 5AAM · UniProt U3N5N6
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