Research workbench
Cryo-EM structure of immature dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 5.0 (class I particle)
Analyse Cryo-EM structure of immature dengue virus serotype 3 in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IDK
- Type
- protein
- Length
- 2,145 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein; Premembrane protein; Fab 1H10 heavy chain (V-region); Fab 1H10 light…
- UniProt
- A9LID6
- Pockets
- 8 · best druggability 0.40
Structure
electron microscopy · 4 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope protein | protein | 394 | 0% helix, 0% strand | A9LID6 |
| D, E, F | Premembrane protein | protein | 79 | 0% helix, 0% strand | A9LID6 |
| H, I, M | Fab 1H10 heavy chain (V-region) | protein | 131 | 0% helix, 0% strand | — |
| J, L, N | Fab 1H10 light chain (V-region) | protein | 111 | 0% helix, 0% strand | — |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.40 | 0.72 | 30 | empty |
| 2 | 112 | 0.38 | 0.72 | 33 | empty |
| 3 | 94 | 0.38 | 0.74 | 20 | empty |
| 4 | 102 | 0.37 | 0.73 | 30 | empty |
| 5 | 70 | 0.32 | 0.73 | 22 | empty |
Interfaces
11 interfaces between chains.
- A–C · 270 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 198 Ų buried · 0 hydrogen bonds · protein-protein
- H–L · 174 Ų buried · 0 hydrogen bonds · protein-protein
- M–N · 174 Ų buried · 0 hydrogen bonds · protein-protein
- I–J · 173 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IDK · Cryo-EM structure of Immature Dengue virus serotype 3 in complex with human antibody 1H10… · 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 A9LID6
- Elsewhere: RCSB PDB 6IDK · PDBe 6IDK · UniProt A9LID6
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