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Crystal structure of dengue 3 virus envelope glycoprotein in complex with the scfv fragment of the broadly neutralizing human antibody EDE1 C10
Analyse Crystal structure of dengue 3 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
- 7A3P
- Type
- protein
- Length
- 1,183 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Single chain variable fragment
- UniProt
- Q07019
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 351 | 8% helix, 51% strand | Q07019 |
| B | Envelope protein E | protein | 361 | 8% helix, 50% strand | Q07019 |
| H | Single chain variable fragment | protein | 125 | 5% helix, 47% strand | — |
| L | Single chain variable fragment | protein | 109 | 3% helix, 48% strand | — |
| I | Single chain variable fragment | protein | 126 | 5% helix, 47% strand | — |
| M | Single chain variable fragment | protein | 111 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.78 | 0.83 | 53 | empty |
| 2 | 734 | 0.75 | 0.80 | 65 | empty |
| 3 | 904 | 0.74 | 0.78 | 83 | empty |
| 4 | 526 | 0.70 | 0.79 | 59 | empty |
| 5 | 125 | 0.47 | 0.78 | 19 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1436 Ų buried · 10 hydrogen bonds · protein-protein
- I–M · 1085 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1010 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 488 Ų buried · 3 hydrogen bonds · protein-protein
- B–M · 440 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7A3P · Crystal structure of dengue 3 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 Q07019
- Elsewhere: RCSB PDB 7A3P · PDBe 7A3P · UniProt Q07019
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