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Cryo-EM structure of dengue virus serotype 2 in complex with the scfv fragment of the broadly neutralizing antibody EDE1 C10
Analyse Cryo-EM structure of dengue virus serotype 2 in complex with the scfv fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CTH
- Type
- protein
- Length
- 2,157 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein; Single chain variable fragment
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- Q88636, Q20II5
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Core protein | protein | 493 | 22% helix, 37% strand | Q88636 |
| B, C | Core protein | protein | 485 | 23% helix, 38% strand | Q88636 |
| F, E | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 75 | 68% helix, 0% strand | Q20II5 |
| D | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 72 | 67% helix, 0% strand | Q20II5 |
| I, H | Single chain variable fragment | protein | 127 | 5% helix, 46% strand | — |
| M, L | Single chain variable fragment | protein | 109 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, I, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.84 | 0.92 | 53 | empty |
| 2 | 1055 | 0.83 | 0.84 | 113 | empty |
| 3 | 582 | 0.80 | 0.86 | 71 | empty |
| 4 | 563 | 0.77 | 0.84 | 67 | empty |
| 5 | 969 | 0.77 | 0.79 | 89 | empty |
Interfaces
20 interfaces between chains.
- C–E · 1674 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1632 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1591 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1546 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1173 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7CTH · Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the… · 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 Q88636
- Every structure of UniProt Q20II5
- Elsewhere: RCSB PDB 7CTH · PDBe 7CTH · UniProt Q88636 · UniProt Q20II5
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