Research workbench
Crystal structure of dengue 1 virus envelope glycoprotein in complex with the scfv fragment of the broadly neutralizing human antibody EDE1 C10
Analyse Crystal structure of dengue 1 virus envelope glycoprotein in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A3O
- Type
- protein
- Length
- 614 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein; Single chain variable fragment (scfv) from antibody EDE1 C10
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- Q9II02
- Ligands
- NAG, FUC, SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 377 | 7% helix, 51% strand | Q9II02 |
| H | Single chain variable fragment (scfv) from antibody EDE1 C10 | protein | 127 | 7% helix, 47% strand | — |
| L | Single chain variable fragment (scfv) from antibody EDE1 C10 | protein | 110 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, L, H
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.63 | 0.74 | 54 | empty |
| 2 | 64 | 0.44 | 0.82 | 24 | empty |
| 3 | 112 | 0.39 | 0.75 | 23 | empty |
| 4 | 106 | 0.38 | 0.75 | 24 | empty |
| 5 | 84 | 0.34 | 0.74 | 15 | SO4 |
Interfaces
3 interfaces between chains.
- H–L · 974 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 354 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 275 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7A3O · Crystal structure of dengue 1 virus envelope glycoprotein in complex with the scFv… · 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 Q9II02
- Elsewhere: RCSB PDB 7A3O · PDBe 7A3O · UniProt Q9II02
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